Dear sir,
I have not yet get answer of my question that how could i maintain cubic
box with periodic boundary condition.
On Tue, Nov 18, 2014 at 1:30 AM, <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
> You can reach the person managing the list at
> amber-owner.ambermd.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: GPU enabled Hardware specification (Ross Walker)
> 2. Re: Failure of antechamber with c -1 m 2 (David A Case)
> 3. Re: Failure of antechamber with c -1 m 2 (Francesco Pietra)
> 4. Re: options "-ext" and "-pqr" of ambpdb are exlusive
> ( LI An-Bang )
> 5. MMPBSA.py nmode (Sourav Purohit)
> 6. 4x GTX 980 (Parker de Waal)
> 7. Re: 4x GTX 980 (James Maier)
> 8. Re: 4x GTX 980 (James Maier)
> 9. Re: Issue with DFTB-MD trajectory (Perry, Jamin W.)
> 10. MMPBSA warning : No skew or curtosis when zero variance in
> moment (Mina Madah)
> 11. Re: GPU enabled Hardware specification (M. Reza Ganjalikhany)
> 12. Re: MMPBSA warning : No skew or curtosis when zero variance
> in moment (Jason Swails)
> 13. Re: MMPBSA.py nmode (Jason Swails)
> 14. Regarding pairdist function in cpptraj (DEBOSTUTI GHOSHDASTIDAR)
> 15. Re: Regarding pairdist function in cpptraj (Daniel Roe)
> 16. Re: Failure of antechamber with c -1 m 2 (David A Case)
> 17. Re: Failure of antechamber with c -1 m 2 (Francesco Pietra)
> 18. Re: help (Robin Jain)
> 19. Re: help (Jason Swails)
> 20. Re: GPU enabled Hardware specification (Ross Walker)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 16 Nov 2014 12:22:46 -0800
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] GPU enabled Hardware specification
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <D08E4742.4CB12%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi Reza,
>
> If you want to play it safe I would suggest the last one in that list -
> GTX780-3GD5 - this is the reference design with NVIDIA's stock heatsink so
> much better tested than the rest which all have weird custom heatsinks
> designed to look k00l.
>
> All the best
> Ross
>
>
>
> On 11/15/14, 11:49 PM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> wrote:
>
> >Dear Ross,
> >
> >Thank you very much, Is the OC make it an unknown issue?
> >Since RMA is not a possible option in my country, I have to be very
> >cautious about the GPU specification before buying it.
> >
> >So I would be very grateful if you could recommend me the appropriate
> >GPU(s) from the following GTX780 list?
> >
> >Here are the different editions of GTX780 which I took from Asus website:
> >ROG POSEIDON-GTX780-P-3GD5
> ><http://www.asus.com/Graphics_Cards/ROG_POSEIDONGTX780P3GD5/>
> >GTX780-DC2OC-3GD5 <http://www.asus.com/Graphics_Cards/GTX780DC2OC3GD5/>
> >STRIX-GTX780-OC-6GD5
> ><http://www.asus.com/Graphics_Cards/STRIXGTX780OC6GD5/>
> >ROG POSEIDON-GTX780-3GD5
> ><http://www.asus.com/Graphics_Cards/ROG_POSEIDONGTX7803GD5/>
> >GTX780-DC2-3GD5 <http://www.asus.com/Graphics_Cards/GTX780DC23GD5/>
> >GTX780-3GD5 <http://www.asus.com/Graphics_Cards/GTX7803GD5/>
> >
> >http://www.asus.com/Graphics_Cards/
> >
> >Regards,
> >
> >On Sun, Nov 16, 2014 at 12:19 AM, Ross Walker <ross.rosswalker.co.uk>
> >wrote:
> >
> >> Hi Reza,
> >>
> >> I have not tried any STRIX branded GPUs - and must admit to not actually
> >> knowing what it stands for. My suggestion would be to suck it and see.
> >> (Asus tend to be a nice brand though).
> >>
> >> Once you receive the GPU run the AMBER validation test on it:
> >> https://dl.dropboxusercontent.com/u/708185/GPU_Validation_Test.tar.gz
> >>
> >> And if all answers do not come out the same - RMA it and got for a
> >>regular
> >> clock (or these days regular OC) card.
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On 11/15/14, 2:41 AM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> >> wrote:
> >>
> >> >How about STRIX OC edition of GTX780?
> >> >Is STRIX edition suitable for GPU accelerated MD?
> >> >
> >> >such as:
> >> >ASUS STRIX-GTX780-OC-6GD5
> >> >GeForce GTX 780 - 6GB - STRIX
> >> >
> >> >On Wed, Oct 29, 2014 at 12:32 AM, Ross Walker <ross.rosswalker.co.uk>
> >> >wrote:
> >> >
> >> >> Agreed - although to caveat that - the GTX780 silicon is fairly
> >>mature
> >> >> these days and from the various hardware I have been testing the
> >> >> superclocked chips actually seem to be okay right now. You should
> >>still
> >> >> test it to be sure but given it is fairly mature silicon the yields
> >>(and
> >> >> thus achievable clock speeds) tend to drift upwards with time. E.g. I
> >> >> certainly would not entertain an overclocked GTX980 right now. But
> >>in a
> >> >> year - maybe...
> >> >>
> >> >> As for brand both Asus and EVGA tend to be pretty good brands so
> >>that's
> >> >> not a worry.
> >> >>
> >> >> All the best
> >> >> Ross
> >> >>
> >> >>
> >> >> On 10/28/14, 12:59 PM, "Scott Le Grand" <varelse2005.gmail.com>
> >>wrote:
> >> >>
> >> >> >Superclocked is a "super" way to get inaccurate results. Avoid...
> >> >> >
> >> >> >
> >> >> >
> >> >> >On Tue, Oct 28, 2014 at 12:50 PM, M. Reza Ganjalikhany <
> >> >> >ganjalikhany.gmail.com> wrote:
> >> >> >
> >> >> >> Thank you very much fro your help.
> >> >> >>
> >> >> >> And the last question:
> >> >> >> Is there any difference between EVGA GTX 780
> >> >> >> <
> >> >> >>
> >> >> >>
> >> >>
> >> >>
> >>
> >>
> http://www.amazon.com/gp/product/B00CTY84KI/ref=as_li_qf_sp_asin_tl?ie=UT
> >> >>
> >>
> >>>>>>F8&camp=211189&creative=373489&creativeASIN=B00CTY84KI&link_code=as3&
> >>>>>>ta
> >> >>>>g=
> >> >> >>freelydownloa-20
> >> >> >> >
> >> >> >> and ASUS GTX 780 (GTX780-3GD5)
> >> >> >> <http://www.asus.com/Graphics_Cards/GTX7803GD5/>?
> >> >> >> It seems that EVGA has superclocked option while ASUS doesn't
> >>have.
> >> >> >> Does superclocked option play an important role in GPU
> >>performance?
> >> >> >>
> >> >> >> On Tue, Oct 28, 2014 at 6:23 PM, Ross Walker
> >><ross.rosswalker.co.uk>
> >> >> >> wrote:
> >> >> >>
> >> >> >> > 780TI is about the same speed as a Titan-Black but (in about
> >>70% of
> >> >> >> cases)
> >> >> >> > gives incorrect numerical answers.
> >> >> >> >
> >> >> >> > 780 on the other hand gives the correct numerical answers.
> >> >> >> >
> >> >> >> > So, my advice is to go with 780 or Titan-Black and avoid 780TI.
> >> >> >> >
> >> >> >> > All the best
> >> >> >> > Ross
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > On 10/28/14, 2:41 AM, "M. Reza Ganjalikhany"
> >> >><ganjalikhany.gmail.com>
> >> >> >> > wrote:
> >> >> >> >
> >> >> >> > >what is the difference between GTX 780 and GTX780Ti in
> >> >>performance?
> >> >> >> > >
> >> >> >> > >On Tue, Oct 28, 2014 at 12:49 AM, Scott Le Grand
> >> >> >><varelse2005.gmail.com
> >> >> >> >
> >> >> >> > >wrote:
> >> >> >> > >
> >> >> >> > >> The successor is the Asus X99-E WS plus Core i7-5930K CPU.
> >> >> >> > >>
> >> >> >> > >>
> >> >> >> > >>
> >> >> >> > >>
> >> >> >> > >>
> >> >> >> > >> On Mon, Oct 27, 2014 at 1:39 PM, M. Reza Ganjalikhany <
> >> >> >> > >> ganjalikhany.gmail.com> wrote:
> >> >> >> > >>
> >> >> >> > >> > Dear Amber Developers,
> >> >> >> > >> >
> >> >> >> > >> > I decided to assemble my own PC with GPU enabled according
> >>to
> >> >> >>your
> >> >> >> > >> website
> >> >> >> > >> > recommendation.
> >> >> >> > >> > Due to some hardware limitations, the recommended
> >>Motherboard
> >> >> >> (P9X79-E
> >> >> >> > >> WS)
> >> >> >> > >> > is not available but other P9X79 families are available
> >>such
> >> >>as
> >> >> >> P9X79
> >> >> >> > >>WS,
> >> >> >> > >> > P9X79 DELUX and P9X79. Is this make the GPU simulation so
> >> >> >>different
> >> >> >> > >>if I
> >> >> >> > >> > use P9X79 WS instead of E WS?
> >> >> >> > >> > What is the main point which should be noticed?
> >> >> >> > >> >
> >> >> >> > >> > Regards,
> >> >> >> > >> > M.Reza
> >> >> >> > >> > _______________________________________________
> >> >> >> > >> > AMBER mailing list
> >> >> >> > >> > AMBER.ambermd.org
> >> >> >> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> > >> >
> >> >> >> > >> _______________________________________________
> >> >> >> > >> AMBER mailing list
> >> >> >> > >> AMBER.ambermd.org
> >> >> >> > >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> > >>
> >> >> >> > >_______________________________________________
> >> >> >> > >AMBER mailing list
> >> >> >> > >AMBER.ambermd.org
> >> >> >> > >http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > AMBER mailing list
> >> >> >> > AMBER.ambermd.org
> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >_______________________________________________
> >> >> >AMBER mailing list
> >> >> >AMBER.ambermd.org
> >> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >_______________________________________________
> >> >AMBER mailing list
> >> >AMBER.ambermd.org
> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 16 Nov 2014 16:20:04 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Failure of antechamber with c -1 m 2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141116212004.GA31947.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Sun, Nov 16, 2014, Francesco Pietra wrote:
> >
> > antechamber -fi pdb -i filename.pdb -fo ac -nc -1 -m 2 -c bcc -o
> > filename.ac -pf y -s
> >
> > reports sqm.out
> > QMMM: System specified with odd number of electrons ( 61)
> > QMMM: but odd spin ( 1). You most likely have the charge of
> > QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> > calculation.
> >
> >
> > There are four N-atoms in the small molecule. Two normal tricoord N, one
> > dicoord N with lone pair, one dicoord N with single electron. I could
> > calculate RESP charges and carried out frequency analysis ab initio HF
> > 6-31G* with a qm package, though still interested in the ac file. Can't
> > understand why with 85 electrons, charge -1 mult 2 is said impossible by
> > antechamber. I am at ambertools 12.
>
> Check the sqm.in file: it looks like antechamber might not be correctly
> passing the "-m " flag info(?).
>
> Also note that bcc charges (and the who antechaber typing scheme) are only
> parameterized for closed shell systems. Since you have (or can get) RESP
> charges, those would seem to best way to go. Setting up force fields for
> organic radicals is uncharted territory, certainly for antechamber.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 16 Nov 2014 22:57:15 +0100
> From: Francesco Pietra <chiendarret.gmail.com>
> Subject: Re: [AMBER] Failure of antechamber with c -1 m 2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEv0nmu4MKTB_=
> SbuKgGZ-Vz2fAgMNmrMhUH1nxpaOitqhjD-w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Professor Case:
>
> Run semi-empirical minimization
> &qmmm
> qm_theory='AM1', grms_tol=0.0002,
> tight_p_conv=1, scfconv=1.d-10, qmcharge=-1,
> /
> 7 N9 31.5580 25.3660 39.2430
> ............................
>
>
> Apparently you are right. I repeated the job, making sure to have inserted
> "-m 2". Could that be fixed?
>
> Although I fully agree with your warning about trying to parameterize
> organic radicals, I tried to have the antechamber output, on which to
> substitute data from the ab initio calculation, as I find it difficult to
> build the entire FF without a layout.
>
> The spin density distribution calculated ab initio agrees fairly well with
> the EPR spectrum, which is encouraging, although the nonbonded remain
> unknown.
>
>
> thanks a lot
>
> francesco pietra
>
>
>
>
>
>
>
> On Sun, Nov 16, 2014 at 10:20 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Sun, Nov 16, 2014, Francesco Pietra wrote:
> > >
> > > antechamber -fi pdb -i filename.pdb -fo ac -nc -1 -m 2 -c bcc -o
> > > filename.ac -pf y -s
> > >
> > > reports sqm.out
> > > QMMM: System specified with odd number of electrons ( 61)
> > > QMMM: but odd spin ( 1). You most likely have the charge of
> > > QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> > > calculation.
> > >
> > >
> > > There are four N-atoms in the small molecule. Two normal tricoord N,
> one
> > > dicoord N with lone pair, one dicoord N with single electron. I could
> > > calculate RESP charges and carried out frequency analysis ab initio HF
> > > 6-31G* with a qm package, though still interested in the ac file.
> Can't
> > > understand why with 85 electrons, charge -1 mult 2 is said impossible
> by
> > > antechamber. I am at ambertools 12.
> >
> > Check the sqm.in file: it looks like antechamber might not be correctly
> > passing the "-m " flag info(?).
> >
> > Also note that bcc charges (and the who antechaber typing scheme) are
> only
> > parameterized for closed shell systems. Since you have (or can get) RESP
> > charges, those would seem to best way to go. Setting up force fields for
> > organic radicals is uncharted territory, certainly for antechamber.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 17 Nov 2014 08:21:34 +0800
> From: " LI An-Bang " <anbangli.qq.com>
> Subject: Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive
> To: " AMBER Mailing List " <amber.ambermd.org>
> Message-ID: <tencent_63C99A631A4C6C3A118C0064.qq.com>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> David,
>
> Thank you for the modified ambpdb program. It works well.
>
> ------------------
> LI AnBang
> Physics Department, Central China Normal University, China
>
>
>
>
>
>
>
> ------------------ Original ------------------
> From: "David A Case";<case.biomaps.rutgers.edu>;
> Date: Fri, Nov 14, 2014 09:19 PM
> To: "AMBER Mailing List"<amber.ambermd.org>;
>
> Subject: Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive
>
>
>
> On Wed, Nov 12, 2014, LI An-Bang wrote:
> >
> > I used ambpdb to generate pdb and pqr files from .prmtop (there is chain
> > ID information) and .inpcrd file, and find that options "-ext" and
> > "-pqr" of ambpdb are exlusive.
>
> Try using the attached ambpdb.F90 file in place of the on that is in
> $AMBERHOME/AmberTools/src/etc. (Be sure to keep a copy of the original.)
> Re-compile and give it a try...not tested, but it looks like it should
> do what you want.
>
> [Aside to Dan: (1) does cpp-ambpdb handle this combination? (2)
> add_pdb.F90
> should be extended to include occupancy and B-factors from the original PDB
> files...we have some upcoming uses for these.]
>
> ...dac
>
> ------------------------------
>
> Message: 5
> Date: Mon, 17 Nov 2014 07:43:37 +0530
> From: Sourav Purohit <sour000.gmail.com>
> Subject: [AMBER] MMPBSA.py nmode
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAFMrzpzV+8ONZOeN1mdQb12TLmThK8FSbAY-YRe4hxyf4QFk+w.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi all,
> For nmode entropy calculation using MMPBSA.py, I obtain warnings like the
> following
> Line minimizer aborted: step at upper bound 0.023143946
> Line minimizer aborted: step at lower bound 1e-20.
>
> What is the difference between the two kinds of warning? What do the upper
> and lower bound refer to?? How are these warnings related to the presence
> of negative normal mode frequencies??
>
> Thanks.
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 17 Nov 2014 02:28:07 +0000
> From: Parker de Waal <Parker.deWaal.vai.org>
> Subject: [AMBER] 4x GTX 980
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <974700F6B71AA04897B9105CC7E1AAFA7D59ED.VAIEXMB01.vai.org>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Everyone,
>
> I apologize for the off topic post, however I'm currently building a 4x
> GTX 980 machine and was wondering if anyone had experience or insight on
> picking a proper case/fans. I'm worried that 4 cards will lead to
> overheating in most traditional cases.
>
> Additionally I'm wondering about the different fans on the GTX 980 cards,
> specifically the reference fan blower vs. the ACX 2.0 fans on the EVGA
> cards.
>
> Any insight would be extremely valuable.
>
> Best,
> Parker
>
>
> ------------------------------
>
> Message: 7
> Date: Sun, 16 Nov 2014 23:13:24 -0500
> From: James Maier <jimbo.maier.gmail.com>
> Subject: Re: [AMBER] 4x GTX 980
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAG6i8VX0fjvbPrA2ZhGP9QWum7L1jtygkHfXhxRDFM1NxiFkTA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Parker,
>
> For the case, you can't go wrong with a HAF or almost anything with a fan
> on the side. We went with the "Thermaltake Overseer" for our cluster; it's
> a bit cheaper than the HAF and has a built-in SATA dock. It's a pretty neat
> case.
> Not that it matters, but the blue lights look exquisite against the green
> GTX logo.
>
> http://www.newegg.com/Product/Product.aspx?Item=N82E16811133194
>
> We actually moved the fan that's pre-installed on the front to the side,
> and put this "bgears b-Blaster" fan in the front instead:
>
> http://www.newegg.com/Product/Product.aspx?item=N82E16835132022
>
> 120 mm, 103 CFM, not too expensive. We've not had any problems with them so
> far after about 9 months.
>
> As for the GPU, we've found the reference blower design to be more
> effective when trying to squeeze four GPUs right next to each other. I
> believe the blower style can generate higher (negative) pressure or
> something, because the ACX, while great on its own, seems to do a terrible
> job when something's directly occluding it. Our ACX GPUs were also higher
> clocked though, so that's an important caveat to anything I wish I could
> tell you more definitively.
>
> But don't take my word for it; consult some BitCoin mining forums---they
> seem to know all about this stuff. I believe a forum like that is where I
> first read something about the reference style being better for >2 GPUs,
> which seems to match our experience.
>
> As Scott has cautioned, "superclocked is a 'super' way to get inaccurate
> results." Sticking with a normal clockspeed will likely save headaches,
> esp. as the 980s are a new design.
>
> The other concern is power; you need a power supply with a rail with enough
> wattage for all cards or with separate rails that all can drive a card. I'm
> not sure if there is a single PSU that can "technically" (on paper,
> following all stats to the letter) drive four GTX780s (require 42 Amps
> each, I've only been able to find +12v with 133.3 Amps, plus about 5 V
> through each PCI slot). If someone knows of an adequate PSU, please correct
> me.
>
> In that regard, the GTX 980s look promising due to their lower power draw.
> There are only 2 issues I can think of atm:
>
> (1) 980s are "provisionally" supported by AMBER. This may not be an issue,
> and according to ambermd.org/gpus there's an optimization coming.
> (2) 980s are immature and thus the silicon is not likely as stable as, say,
> a 780 or a Titan.
>
> I'm guessing Ross, Scott, or anyone who has gotten their hands on some 980s
> can chime in more about the above points.
>
> HTH,
>
> James
>
> On Sun, Nov 16, 2014 at 9:28 PM, Parker de Waal <Parker.deWaal.vai.org>
> wrote:
>
> > Hi Everyone,
> >
> > I apologize for the off topic post, however I'm currently building a 4x
> > GTX 980 machine and was wondering if anyone had experience or insight on
> > picking a proper case/fans. I'm worried that 4 cards will lead to
> > overheating in most traditional cases.
> >
> > Additionally I'm wondering about the different fans on the GTX 980 cards,
> > specifically the reference fan blower vs. the ACX 2.0 fans on the EVGA
> > cards.
> >
> > Any insight would be extremely valuable.
> >
> > Best,
> > Parker
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 8
> Date: Sun, 16 Nov 2014 23:16:18 -0500
> From: James Maier <jimbo.maier.gmail.com>
> Subject: Re: [AMBER] 4x GTX 980
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAG6i8VX6V=8boLc=tcingjAjjoJ+9xyg=
> sO1+61HJ9SrE84eUQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> **Please note that all experiences I've cited are for GTX 780s.
>
> On Sun, Nov 16, 2014 at 11:13 PM, James Maier <jimbo.maier.gmail.com>
> wrote:
>
> > Hi Parker,
> >
> > For the case, you can't go wrong with a HAF or almost anything with a fan
> > on the side. We went with the "Thermaltake Overseer" for our cluster;
> it's
> > a bit cheaper than the HAF and has a built-in SATA dock. It's a pretty
> neat
> > case.
> > Not that it matters, but the blue lights look exquisite against the green
> > GTX logo.
> >
> > http://www.newegg.com/Product/Product.aspx?Item=N82E16811133194
> >
> > We actually moved the fan that's pre-installed on the front to the side,
> > and put this "bgears b-Blaster" fan in the front instead:
> >
> > http://www.newegg.com/Product/Product.aspx?item=N82E16835132022
> >
> > 120 mm, 103 CFM, not too expensive. We've not had any problems with them
> > so far after about 9 months.
> >
> > As for the GPU, we've found the reference blower design to be more
> > effective when trying to squeeze four GPUs right next to each other. I
> > believe the blower style can generate higher (negative) pressure or
> > something, because the ACX, while great on its own, seems to do a
> terrible
> > job when something's directly occluding it. Our ACX GPUs were also higher
> > clocked though, so that's an important caveat to anything I wish I could
> > tell you more definitively.
> >
> > But don't take my word for it; consult some BitCoin mining forums---they
> > seem to know all about this stuff. I believe a forum like that is where I
> > first read something about the reference style being better for >2 GPUs,
> > which seems to match our experience.
> >
> > As Scott has cautioned, "superclocked is a 'super' way to get inaccurate
> > results." Sticking with a normal clockspeed will likely save headaches,
> > esp. as the 980s are a new design.
> >
> > The other concern is power; you need a power supply with a rail with
> > enough wattage for all cards or with separate rails that all can drive a
> > card. I'm not sure if there is a single PSU that can "technically" (on
> > paper, following all stats to the letter) drive four GTX780s (require 42
> > Amps each, I've only been able to find +12v with 133.3 Amps, plus about
> 5 V
> > through each PCI slot). If someone knows of an adequate PSU, please
> correct
> > me.
> >
> > In that regard, the GTX 980s look promising due to their lower power
> draw.
> > There are only 2 issues I can think of atm:
> >
> > (1) 980s are "provisionally" supported by AMBER. This may not be an
> issue,
> > and according to ambermd.org/gpus there's an optimization coming.
> > (2) 980s are immature and thus the silicon is not likely as stable as,
> > say, a 780 or a Titan.
> >
> > I'm guessing Ross, Scott, or anyone who has gotten their hands on some
> > 980s can chime in more about the above points.
> >
> > HTH,
> >
> > James
> >
> > On Sun, Nov 16, 2014 at 9:28 PM, Parker de Waal <Parker.deWaal.vai.org>
> > wrote:
> >
> >> Hi Everyone,
> >>
> >> I apologize for the off topic post, however I'm currently building a 4x
> >> GTX 980 machine and was wondering if anyone had experience or insight on
> >> picking a proper case/fans. I'm worried that 4 cards will lead to
> >> overheating in most traditional cases.
> >>
> >> Additionally I'm wondering about the different fans on the GTX 980
> cards,
> >> specifically the reference fan blower vs. the ACX 2.0 fans on the EVGA
> >> cards.
> >>
> >> Any insight would be extremely valuable.
> >>
> >> Best,
> >> Parker
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 17 Nov 2014 06:19:05 +0000
> From: "Perry, Jamin W." <PerryJam.missouri.edu>
> Subject: Re: [AMBER] Issue with DFTB-MD trajectory
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> C0AE854CFD64164BA01F40E938BDB1BE10CAB7C8.UM-MBX-N02.um.umsystem.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> David,
>
> Thank you for your response. I took your advice of extensive output from a
> serial compilation of the code and found a some distortion in the system
> that appears anomalous and could be a the tell-tell sign of my silent SCF
> failure. Thank you again.
>
> Jamin
>
>
>
> ________________________________________
> From: David A Case [case.biomaps.rutgers.edu]
> Sent: Tuesday, November 11, 2014 5:56 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Issue with DFTB-MD trajectory
>
> On Sun, Nov 09, 2014, Perry, Jamin W. wrote:
> >
> > I am attempting to calculate a QM/MM trajectory with Sander (released
> > with Ambertools14) using SCC-DFTB to represent the quantum region.
> > The trajectory successfully integrates for about 250 steps and then
> > the program appears to hang without exiting or producing any error
> > messages. Is anyone familiar with this sort of error? I appreciate any
> > assistance that can be offered. My input control file to Sander can be
> > found below.
>
> It is certainly possible that the system may come to some configuration
> where
> the SCF procedure no longer converges. Be sure you are running in serial
> mode, set ntpr=ntwx=1, and do a short simulation of 500 steps or so (which
> will presumably fail around step 250. Examine the energetics and geometry
> near the point of failure.
>
> ...good luck....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 17 Nov 2014 11:53:22 +0330
> From: Mina Madah <madahmina.gmail.com>
> Subject: [AMBER] MMPBSA warning : No skew or curtosis when zero
> variance in moment
> To: amber.ambermd.org
> Message-ID:
> <
> CAJDA_zXjO0onfA1B+VcVaLBHLwy7hEkWqwiwOvoqAdjSk1ViKA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all
> I am performing mmpbsa calculation for DNA-ligand (amber 10). I face whit
> two problem through running and analyzing:
>
> 1. when running mm_pbsa.pl, this massage is appeared:
>
> No skew or curtosis when zero variance in moment
> No skew or curtosis when zero variance in moment
> No skew or curtosis when zero variance in moment
>
> after termination, and get the snapshot_statistics.out, I check the
> snapshot_com.all.out,
> no massages or strange word is observed. By watching binding_energy.log
> file,
> this warning is written in it:
>
> Reading snapshot_rec.all.out
> Checking consistency of CALC
> Checking consistency of DATA
> Entry 1 NM SROT 0 exists -> overwriting
> Entry 1 NM SROT 1 exists -> overwriting
>
> Should I concern or ignore this warning? and how can I fix it?
>
> 2. Energy decomposition in snapshot_statistics.out shows unreliable data
> such
> as:
> VDW energy is positive, and INT energy is not zero?
> system consists of DNA, ligand and Na+ ions. Simulation is done in explicit
> solvent for 5 ns.
>
> here is my binding_energy.mmpbsa file:
>
> #
> # Input parameters for mm_pbsa.pl
> #
> # Holger Gohlke
> # 15.02.2012
> #
>
> ################################################################################
> .GENERAL
> #
> # General parameters
> # 0: means NO; >0: means YES
> #
> # mm_pbsa allows to calculate (absolute) free energies for one molecular
> # species or a free energy difference according to:
> #
> # Receptor + Ligand = Complex,
> # DeltaG = G(Complex) - G(Receptor) - G(Ligand).
> #
> # VERBOSE - If set to 1, input and output files are not removed. This is
> # useful for debugging purposes.
> # PARALLEL - If set to values > 1, energy calculations for snapshots are
> # done in parallel, using PARALLEL number of threads.
> #
> # PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during
> # generation of snapshots as well as during mm_pbsa
> calculations.
> # PATH - Specifies the location where to store or get snapshots.
> # START - Specifies the first snapshot to be used in energy calculations
> # (optional, defaults to 1).
> # STOP - Specifies the last snapshot to be used in energy calculations
> # (optional, defaults to 10e10).
> # OFFSET - Specifies the offset between snapshots in energy calculations
> # (optional, defaults to 1).
> #
> # COMPLEX - Set to 1 if free energy difference is calculated.
> # RECEPTOR - Set to 1 if either (absolute) free energy or free energy
> # difference are calculated.
> # LIGAND - Set to 1 if free energy difference is calculated.
> #
> # COMPT - parmtop file for the complex (not necessary for option GC).
> # RECPT - parmtop file for the receptor (not necessary for option GC).
> # LIGPT - parmtop file for the ligand (not necessary for option GC).
> #
> # GC - Snapshots are generated from trajectories (see below).
> # AS - Residues are mutated to Ala during generation of snapshots from
> # trajectories.
> # DC - Decompose the free energies into individual contributions.
> # (When using DC, MM and GB must be set to 1, even if a PB
> decomposition
> # is also requested.)
> #
> # MM - Calculation of gas phase energies using sander.
> # GB - Calculation of desolvation free energies using the GB models in
> sander
> # (see below).
> # PB - Calculation of desolvation free energies using the PB method and
> # computation of nonpolar solvation free energies according to
> # the INP option in pbsa (see below).
> # MS - Calculation of nonpolar contributions to desolvation using molsurf
> # (see below).
> # If MS == 0 and GB == 1, nonpolar contributions are calculated
> either
> # with the LCPO (GBSA == 1) or the ICOSA (GBSA == 2) method in
> sander
> # (see below).
> # If MS == 0 and PB == 1, nonpolar contributions are calculated
> according
> # the INP option in pbsa (see below).
> # NM - Calculation of entropies with nmode.
> #
> VERBOSE 0
> PARALLEL 0
> #
> PREFIX snapshot
> PATH ./
> START 400
> STOP 500
> OFFSET 1
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./dna-ox.prmtop
> RECPT ./dna.prmtop
> LIGPT ./lig.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 1
> PB 1
> MS 1
> #
> NM 1
> #
>
> ################################################################################
> .PB
> #
> # PB parameters (this section is only relevant if PB = 1 above)
> #
> # The following parameters are passed to the PB solver.
> # Additional input parameters may also be added here. See the sander PB
> # documentation for more options.
> #
> # PROC - Determines which program is used for solving the PB equation:
> # Delphi (PROC == 1), PBSA (PROC == 2), or APBS (PROC == 3).
> # By default, PROC == 2, the pbsa program of the AMBER suite is
> used.
> # REFE - Determines which reference state is taken for PB calc:
> # By default, REFE == 0, reaction field energy is calculated with
> # EXDI/INDI. Here, INDI must agree with DIELC from MM part.
> # INDI - Dielectric constant for the solute.
> # EXDI - Dielectric constant for the surrounding solvent.
> # ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.
> # SCALE - Lattice spacing in no. of grids per Angstrom.
> # LINIT - No. of iterations with linear PB equation.
> # RADIOPT - Option to set up radii for PB calc:
> # 0: uses the radii from the prmtop file. Default.
> # 1: uses the radii optimized by Tan and Luo with respect to
> the
> # reaction field energies computed in the TIP3P explicit
> solvents
> # (Tan & Luo, J. Phys. Chem. B, 2006, 110, 18680-18687).
> # Note that optimized radii are based on AMBER atom types
> # (upper case) and charges. Radii from the prmtop files are
> used
> # if the atom types are defined by antechamber (lower case).
> # ARCRES - Resolution (in the unit of Angstrom) of solvent accessible
> arcs
> # IVCAP - If set to 1, a solvent sphere (specified by CUTCAP,XCAP,YCAP,
> # and ZCAP) is excised from a box of water. If set to 5, a
> solvent
> # shell is excised, specified by CUTCAP (the thickness of the
> shell
> # in A). The electrostatic part of the solvation free energy is
> # estimated from a linear response approximation using the
> explicit
> # solvent plus a reaction field contribution from outside the
> sphere
> # (i.e., a hybrid solvation approach is pursued).
> # In addition, the nonpolar contribution is estimated from a sum
> of
> # (attractive) dispersion interactions calc. between the solute
> and
> # the solvent molecules plus a (repulsive) cavity contribution
> # (Gohlke & Case, J. comput. Chem. 2004, 25, 238-250).
> # For the latter, the surface calculation must be done with MS =
> 1 and
> # the PROBE should be set to 1.4 to get the solvent excluded
> surface.
> # In this case bondi radii are used as cavity radii set.
> # CUTCAP - Radius of the water sphere or thickness of the water shell.
> # Note that the sphere must enclose the whole solute.
> # XCAP - Location of the center of the water sphere.
> # YCAP
> # ZCAP
> #
> # NP Parameters for nonpolar solvation energies if MS = 0
> #
> # INP - Option for modeling nonpolar solvation free energy.
> # See sander PB documentation for more information on the
> # implementations by Tan and Luo.
> # 1: uses the solvent-accessible-surface area to correlate total
> # nonpolar solvation free energy:
> # Gnp = SURFTEN * SASA + SURFOFF. Default.
> # 2: uses the solvent-accessible-surface area to correlate the
> # repulsive (cavity) term only, and uses a surface-integration
> # approach to compute the attractive (dispersion) term:
> # Gnp = Gdisp + Gcavity
> # = Gdisp + SURFTEN * SASA + SURFOFF.
> # When this option is used, RADIOPT has to be set to 1,
> # i.e. the radii set optimized by Tan and Luo.
> # SURFTEN/SURFOFF - Values used to compute the nonpolar
> # solvation free energy Gnp acccording to INP.
> # If INP = 1 and RADIOPT = 0 (default, see above),
> # use SURFTEN/SURFOFF parameters that fit with the radii from the
> # prmtop file, e.g.,
> # use SURFTEN: 0.00542 and SURFOFF: 0.92 for PARSE radii.
> # If INP = 2 and RADIOPT = 1, please set these to the following:
> # SURFTEN: 0.0378; OFFSET: -0.5692
> #
> # NP Parameters for nonpolar solvation energies if MS = 1
> #
> # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp
> to
> # the desolvation according to:
> # (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP == 0)
> # Use parameters that fit with the radii from the reaction field
> # calculation. E.g., use SURFTEN: 0.00542, SURFOFF: 0.92 for
> # PARSE radii
> # (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF (IVCAP
> > 0)
> # Nonpolar solvation free energy calculated as discribed for
> IVCAP > 0
> # above. In this case use SURFTEN: 0.069; SURFOFF: 0.00 for
> # calculating the Gcavity contribution.
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 5
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> ARCRES 0.0625
> INP 1
> #
> SURFTEN 0.005
> SURFOFF 0.00
> #
> IVCAP 0
> CUTCAP -1.0
> XCAP 0.0
> YCAP 0.0
> ZCAP 0.0
> #
>
> ################################################################################
> .MM
> #
> # MM parameters (this section is only relevant if MM = 1 above)
> #
> # The following parameters are passed to sander.
> # For further details see the sander documentation.
> #
> # DIELC - Dielectricity constant for electrostatic interactions.
> # Note: This is not related to GB calculations.
> #
> DIELC 1.0
> #
>
> ################################################################################
> .GB
> #
> # GB parameters (this section is only relevant if GB = 1 above)
> #
> # The first group of the following parameters are passed to sander.
> # For further details see the sander documentation.
> #
> # IGB - Switches between Tsui's GB (1) and Onufriev's GB (2, 5).
> # GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.
> # Decomposition only works with ICOSA.
> # SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
> # EXTDIEL - Dielectricity constant for the solvent.
> # INTDIEL - Dielectricity constant for the solute.
> #
> # SURFTEN / SURFOFF - Values used to compute the nonpolar contribution
> Gnp to
> # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
> # Choose SURFTEN and SURFOFF values according to the selected
> # GB model, e.g.:
> # IGB=1 : SURFTEN=0.0072, SURFOFF=0.0, mbondi radii
> # (Tsui & Case, Biopolymers 2000, 56, 275-291)
> # IGB=2 : SURFTEN=0.005, SURFOFF=0.0, mbondi2 radii
> # (Onufriev et al, Proteins 2004, 55, 383-394)
> # IGB=5 : SURFTEN=0.005, SURFOFF=0.0, mbondi2 radii
> # (Onufriev et al, Proteins 2004, 55, 383-394)
> #
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.005
> SURFOFF 0.00
> #
>
> ################################################################################
> .MS
> #
> # Molsurf parameters (this section is only relevant if MS = 1 above)
> #
> # PROBE - Radius of the probe sphere used to calculate the SAS.
> # In general, since Bondi radii are already augmented by 1.4A,
> # PROBE should be 0.0
> # In IVCAP = 1 or 5, the solvent excluded surface is required for
> # calculating the cavity contribution. Bondi radii are not
> # augmented in this case and PROBE should be 1.4.
> #
> PROBE 0.0
> #
>
> ################################################################################
> .NM
> #
> # Parameters for sander/nmode calculation (this section is only relevant if
> NM = 1 above)
> #
> # The following parameters are passed to sander (for minimization) and
> nmode
> # (for entropy calculation using gasphase statistical mechanics).
> # For further details see documentation.
> #
> # DIELC - (Distance-dependent) dielectric constant
> # MAXCYC - Maximum number of cycles of minimization.
> # DRMS - Convergence criterion for the energy gradient.
> #
> DIELC 4
> MAXCYC 1000
> DRMS 0.1
> #
>
> ################################################################################
> .PROGRAMS
> #
> # Additional program executables can be defined here
> #
>
> ################################################################################
>
>
> Any help is appreciated.
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 17 Nov 2014 12:47:18 +0330
> From: "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> Subject: Re: [AMBER] GPU enabled Hardware specification
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CACQTqGVC1tsK6Pf8LKXhtsdsaMLuGBTQYp1kHSh3YDgnLOYE7w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> According to their documents the new heatsink design enhanced the cooling
> performance much better than the reference design.
>
> Apart from its weird cooling system, GTX780-DC2-3GD5 (which is similar to
> the reference design GTX780-3GD3), is available for me to buy. But I am
> not sure that, this is a reliable GPU for MD or it is better to seek for
> the GTX780-3GD3.
>
> On Sun, Nov 16, 2014 at 11:52 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi Reza,
> >
> > If you want to play it safe I would suggest the last one in that list -
> > GTX780-3GD5 - this is the reference design with NVIDIA's stock heatsink
> so
> > much better tested than the rest which all have weird custom heatsinks
> > designed to look k00l.
> >
> > All the best
> > Ross
> >
> >
> >
> > On 11/15/14, 11:49 PM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> > wrote:
> >
> > >Dear Ross,
> > >
> > >Thank you very much, Is the OC make it an unknown issue?
> > >Since RMA is not a possible option in my country, I have to be very
> > >cautious about the GPU specification before buying it.
> > >
> > >So I would be very grateful if you could recommend me the appropriate
> > >GPU(s) from the following GTX780 list?
> > >
> > >Here are the different editions of GTX780 which I took from Asus
> website:
> > >ROG POSEIDON-GTX780-P-3GD5
> > ><http://www.asus.com/Graphics_Cards/ROG_POSEIDONGTX780P3GD5/>
> > >GTX780-DC2OC-3GD5 <http://www.asus.com/Graphics_Cards/GTX780DC2OC3GD5/>
> > >STRIX-GTX780-OC-6GD5
> > ><http://www.asus.com/Graphics_Cards/STRIXGTX780OC6GD5/>
> > >ROG POSEIDON-GTX780-3GD5
> > ><http://www.asus.com/Graphics_Cards/ROG_POSEIDONGTX7803GD5/>
> > >GTX780-DC2-3GD5 <http://www.asus.com/Graphics_Cards/GTX780DC23GD5/>
> > >GTX780-3GD5 <http://www.asus.com/Graphics_Cards/GTX7803GD5/>
> > >
> > >http://www.asus.com/Graphics_Cards/
> > >
> > >Regards,
> > >
> > >On Sun, Nov 16, 2014 at 12:19 AM, Ross Walker <ross.rosswalker.co.uk>
> > >wrote:
> > >
> > >> Hi Reza,
> > >>
> > >> I have not tried any STRIX branded GPUs - and must admit to not
> actually
> > >> knowing what it stands for. My suggestion would be to suck it and see.
> > >> (Asus tend to be a nice brand though).
> > >>
> > >> Once you receive the GPU run the AMBER validation test on it:
> > >> https://dl.dropboxusercontent.com/u/708185/GPU_Validation_Test.tar.gz
> > >>
> > >> And if all answers do not come out the same - RMA it and got for a
> > >>regular
> > >> clock (or these days regular OC) card.
> > >>
> > >> All the best
> > >> Ross
> > >>
> > >>
> > >>
> > >> On 11/15/14, 2:41 AM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> > >> wrote:
> > >>
> > >> >How about STRIX OC edition of GTX780?
> > >> >Is STRIX edition suitable for GPU accelerated MD?
> > >> >
> > >> >such as:
> > >> >ASUS STRIX-GTX780-OC-6GD5
> > >> >GeForce GTX 780 - 6GB - STRIX
> > >> >
> > >> >On Wed, Oct 29, 2014 at 12:32 AM, Ross Walker <ross.rosswalker.co.uk
> >
> > >> >wrote:
> > >> >
> > >> >> Agreed - although to caveat that - the GTX780 silicon is fairly
> > >>mature
> > >> >> these days and from the various hardware I have been testing the
> > >> >> superclocked chips actually seem to be okay right now. You should
> > >>still
> > >> >> test it to be sure but given it is fairly mature silicon the yields
> > >>(and
> > >> >> thus achievable clock speeds) tend to drift upwards with time.
> E.g. I
> > >> >> certainly would not entertain an overclocked GTX980 right now. But
> > >>in a
> > >> >> year - maybe...
> > >> >>
> > >> >> As for brand both Asus and EVGA tend to be pretty good brands so
> > >>that's
> > >> >> not a worry.
> > >> >>
> > >> >> All the best
> > >> >> Ross
> > >> >>
> > >> >>
> > >> >> On 10/28/14, 12:59 PM, "Scott Le Grand" <varelse2005.gmail.com>
> > >>wrote:
> > >> >>
> > >> >> >Superclocked is a "super" way to get inaccurate results. Avoid...
> > >> >> >
> > >> >> >
> > >> >> >
> > >> >> >On Tue, Oct 28, 2014 at 12:50 PM, M. Reza Ganjalikhany <
> > >> >> >ganjalikhany.gmail.com> wrote:
> > >> >> >
> > >> >> >> Thank you very much fro your help.
> > >> >> >>
> > >> >> >> And the last question:
> > >> >> >> Is there any difference between EVGA GTX 780
> > >> >> >> <
> > >> >> >>
> > >> >> >>
> > >> >>
> > >> >>
> > >>
> > >>
> >
> http://www.amazon.com/gp/product/B00CTY84KI/ref=as_li_qf_sp_asin_tl?ie=UT
> > >> >>
> > >>
> >
> >>>>>>F8&camp=211189&creative=373489&creativeASIN=B00CTY84KI&link_code=as3&
> > >>>>>>ta
> > >> >>>>g=
> > >> >> >>freelydownloa-20
> > >> >> >> >
> > >> >> >> and ASUS GTX 780 (GTX780-3GD5)
> > >> >> >> <http://www.asus.com/Graphics_Cards/GTX7803GD5/>?
> > >> >> >> It seems that EVGA has superclocked option while ASUS doesn't
> > >>have.
> > >> >> >> Does superclocked option play an important role in GPU
> > >>performance?
> > >> >> >>
> > >> >> >> On Tue, Oct 28, 2014 at 6:23 PM, Ross Walker
> > >><ross.rosswalker.co.uk>
> > >> >> >> wrote:
> > >> >> >>
> > >> >> >> > 780TI is about the same speed as a Titan-Black but (in about
> > >>70% of
> > >> >> >> cases)
> > >> >> >> > gives incorrect numerical answers.
> > >> >> >> >
> > >> >> >> > 780 on the other hand gives the correct numerical answers.
> > >> >> >> >
> > >> >> >> > So, my advice is to go with 780 or Titan-Black and avoid
> 780TI.
> > >> >> >> >
> > >> >> >> > All the best
> > >> >> >> > Ross
> > >> >> >> >
> > >> >> >> >
> > >> >> >> >
> > >> >> >> > On 10/28/14, 2:41 AM, "M. Reza Ganjalikhany"
> > >> >><ganjalikhany.gmail.com>
> > >> >> >> > wrote:
> > >> >> >> >
> > >> >> >> > >what is the difference between GTX 780 and GTX780Ti in
> > >> >>performance?
> > >> >> >> > >
> > >> >> >> > >On Tue, Oct 28, 2014 at 12:49 AM, Scott Le Grand
> > >> >> >><varelse2005.gmail.com
> > >> >> >> >
> > >> >> >> > >wrote:
> > >> >> >> > >
> > >> >> >> > >> The successor is the Asus X99-E WS plus Core i7-5930K CPU.
> > >> >> >> > >>
> > >> >> >> > >>
> > >> >> >> > >>
> > >> >> >> > >>
> > >> >> >> > >>
> > >> >> >> > >> On Mon, Oct 27, 2014 at 1:39 PM, M. Reza Ganjalikhany <
> > >> >> >> > >> ganjalikhany.gmail.com> wrote:
> > >> >> >> > >>
> > >> >> >> > >> > Dear Amber Developers,
> > >> >> >> > >> >
> > >> >> >> > >> > I decided to assemble my own PC with GPU enabled
> according
> > >>to
> > >> >> >>your
> > >> >> >> > >> website
> > >> >> >> > >> > recommendation.
> > >> >> >> > >> > Due to some hardware limitations, the recommended
> > >>Motherboard
> > >> >> >> (P9X79-E
> > >> >> >> > >> WS)
> > >> >> >> > >> > is not available but other P9X79 families are available
> > >>such
> > >> >>as
> > >> >> >> P9X79
> > >> >> >> > >>WS,
> > >> >> >> > >> > P9X79 DELUX and P9X79. Is this make the GPU simulation
> so
> > >> >> >>different
> > >> >> >> > >>if I
> > >> >> >> > >> > use P9X79 WS instead of E WS?
> > >> >> >> > >> > What is the main point which should be noticed?
> > >> >> >> > >> >
> > >> >> >> > >> > Regards,
> > >> >> >> > >> > M.Reza
> > >> >> >> > >> > _______________________________________________
> > >> >> >> > >> > AMBER mailing list
> > >> >> >> > >> > AMBER.ambermd.org
> > >> >> >> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >> > >> >
> > >> >> >> > >> _______________________________________________
> > >> >> >> > >> AMBER mailing list
> > >> >> >> > >> AMBER.ambermd.org
> > >> >> >> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >> > >>
> > >> >> >> > >_______________________________________________
> > >> >> >> > >AMBER mailing list
> > >> >> >> > >AMBER.ambermd.org
> > >> >> >> > >http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >> >
> > >> >> >> >
> > >> >> >> >
> > >> >> >> > _______________________________________________
> > >> >> >> > AMBER mailing list
> > >> >> >> > AMBER.ambermd.org
> > >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >> >
> > >> >> >> _______________________________________________
> > >> >> >> AMBER mailing list
> > >> >> >> AMBER.ambermd.org
> > >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >>
> > >> >> >_______________________________________________
> > >> >> >AMBER mailing list
> > >> >> >AMBER.ambermd.org
> > >> >> >http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> >>
> > >> >>
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> >_______________________________________________
> > >> >AMBER mailing list
> > >> >AMBER.ambermd.org
> > >> >http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >_______________________________________________
> > >AMBER mailing list
> > >AMBER.ambermd.org
> > >http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 17 Nov 2014 08:57:32 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA warning : No skew or curtosis when zero
> variance in moment
> To: amber.ambermd.org
> Message-ID: <1416232652.2536.1.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2014-11-17 at 11:53 +0330, Mina Madah wrote:
> > Dear all
> > I am performing mmpbsa calculation for DNA-ligand (amber 10). I face
> whit
> > two problem through running and analyzing:
>
> I suggest upgrading to AmberTools 14, which provides better error
> messages and is overall better supported.
>
> > 1. when running mm_pbsa.pl, this massage is appeared:
> >
> > No skew or curtosis when zero variance in moment
> > No skew or curtosis when zero variance in moment
> > No skew or curtosis when zero variance in moment
>
> The kurtosis and skew are the 3rd and 4th moments of a distribution (the
> mean and variance being the first two). If the variance is zero (which
> happens when, for instance, you only have one data point or all data
> points are the same), then all moments after the variance are zero as
> well, and every value is exactly equal to the mean (i.e., the
> distribution function is a delta function).
>
> > after termination, and get the snapshot_statistics.out, I check the
> > snapshot_com.all.out,
> > no massages or strange word is observed. By watching binding_energy.log
> file,
> > this warning is written in it:
> >
> > Reading snapshot_rec.all.out
> > Checking consistency of CALC
> > Checking consistency of DATA
> > Entry 1 NM SROT 0 exists -> overwriting
> > Entry 1 NM SROT 1 exists -> overwriting
> >
> > Should I concern or ignore this warning? and how can I fix it?
>
> This is one example of where the error message is improved. You are
> pointed to this website for this error message:
> http://ambermd.org/Questions/mm_pbsa.html#read_data_exists_overwriting
>
> >
> > 2. Energy decomposition in snapshot_statistics.out shows unreliable data
> such
> > as:
> > VDW energy is positive, and INT energy is not zero?
> > system consists of DNA, ligand and Na+ ions. Simulation is done in
> explicit
> > solvent for 5 ns.
>
> I fail to see why this data is "wrong" or "unreliable". It's perfectly
> possible for the net vdW interactions between two residues to be
> positive if there is a steric clash (that would be offset by other more
> attractive terms). Also, certain internal energies *will* be non-zero
> depending on your simulation settings, but you never told us what kind
> of decomposition calculation you were running or which values turned out
> positive, so I can only speculate.
>
> I would suggest upgrading to AmberTools 14 and using MMPBSA.py, which I
> (and others that respond on this list) am better able to help with.
> And, as always, provide more information about *exactly* what you have
> done and the *exact* problems you are having so we don't have to guess
> those details.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 13
> Date: Mon, 17 Nov 2014 09:02:28 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] MMPBSA.py nmode
> To: amber.ambermd.org
> Message-ID: <1416232948.2536.3.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2014-11-17 at 07:43 +0530, Sourav Purohit wrote:
> > Hi all,
> > For nmode entropy calculation using MMPBSA.py, I obtain warnings like the
> > following
> > Line minimizer aborted: step at upper bound 0.023143946
> > Line minimizer aborted: step at lower bound 1e-20.
> >
> > What is the difference between the two kinds of warning? What do the
> upper
> > and lower bound refer to??
>
> They have something to do with the minimizer getting "stuck" -- I'm not
> sure exactly what the numbers mean.
>
> > How are these warnings related to the presence
> > of negative normal mode frequencies??
>
> It means that the minimizer got stuck and could not get to a "true"
> minimum. Since it's not at a true minimum (and may in fact be kind of
> far away from one), you get some negative frequencies.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Mon, 17 Nov 2014 20:19:06 +0530
> From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
> Subject: [AMBER] Regarding pairdist function in cpptraj
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAJYAmDWOGe2cqi9Tz==
> r_+e1t6Tvq40ADpeytNor3dSD0nws3Q.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Amber Users
>
> I was trying to use pairdist function to compute the distribution of
> distance between two sets of atoms. So the command I gave was as follows:
>
> pairdist out ring :MOL.N1,N2,C1,C2,C3 :MOL.N1,N2,C1,C2,C3 0.1
>
> However on execution i get an error saying
> Error: pairdist: No mask1 specified.
>
> Is there a particular way of specifying the mask? Couldn't figure out from
> the manual.
>
> Also, when I give a set of atoms, does the function consider the
> center-of-mass?
>
> Thanks for any help
>
> --
> Debostuti Ghosh Dastidar
> Department of Biotechnology
> Indian Institute of Technology Madras
>
>
> ------------------------------
>
> Message: 15
> Date: Mon, 17 Nov 2014 08:17:31 -0700
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Regarding pairdist function in cpptraj
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZERWVC=
> GjduEW6G6oiBmLmgv_XMH7hmWMmq4PxUS6URw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You need to use the 'mask' and 'mask2' keywords to specify your masks.
> The onboard help shows the correct syntax:
>
> > help pairdist
> out <filename> mask <mask> [mask2 <mask>] [<resolution> delta]
> Calculate pair distribution function P(r) between two masks.
>
> Hope this helps,
>
> -Dan
>
>
> On Mon, Nov 17, 2014 at 7:49 AM, DEBOSTUTI GHOSHDASTIDAR
> <debostutighosh.gmail.com> wrote:
> > Dear Amber Users
> >
> > I was trying to use pairdist function to compute the distribution of
> > distance between two sets of atoms. So the command I gave was as follows:
> >
> > pairdist out ring :MOL.N1,N2,C1,C2,C3 :MOL.N1,N2,C1,C2,C3 0.1
> >
> > However on execution i get an error saying
> > Error: pairdist: No mask1 specified.
> >
> > Is there a particular way of specifying the mask? Couldn't figure out
> from
> > the manual.
> >
> > Also, when I give a set of atoms, does the function consider the
> > center-of-mass?
> >
> > Thanks for any help
> >
> > --
> > Debostuti Ghosh Dastidar
> > Department of Biotechnology
> > Indian Institute of Technology Madras
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
>
> ------------------------------
>
> Message: 16
> Date: Mon, 17 Nov 2014 11:01:25 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Failure of antechamber with c -1 m 2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20141117160125.GA50331.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Sun, Nov 16, 2014, Francesco Pietra wrote:
> >
> > Run semi-empirical minimization
> > &qmmm
> > qm_theory='AM1', grms_tol=0.0002,
> > tight_p_conv=1, scfconv=1.d-10, qmcharge=-1,
> > /
> > 7 N9 31.5580 25.3660 39.2430
> > ............................
> >
> >
> > Apparently you are right. I repeated the job, making sure to have
> inserted
> > "-m 2". Could that be fixed?
>
> > Although I fully agree with your warning about trying to parameterize
> > organic radicals, I tried to have the antechamber output, on which to
> > substitute data from the ab initio calculation, as I find it difficult to
> > build the entire FF without a layout.
>
> For now, why not just run antechamber without the -bcc flag? That will
> give
> you all the files, just without the (rather incorrect) am1-bcc charges.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 17
> Date: Mon, 17 Nov 2014 17:55:07 +0100
> From: Francesco Pietra <chiendarret.gmail.com>
> Subject: Re: [AMBER] Failure of antechamber with c -1 m 2
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEv0nmtArA4GEOsTUYJMEjD70NLu7YFu+U-UqhSYOksLFcTMsQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> > For now, why not just run antechamber without the -bcc flag? That will
> > give
> > you all the files, just without the (rather incorrect) am1-bcc charges.
> >
>
> I can only regret for my short imagination, while thanking you very much.
> francesco
>
> On Mon, Nov 17, 2014 at 5:01 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > On Sun, Nov 16, 2014, Francesco Pietra wrote:
> > >
> > > Run semi-empirical minimization
> > > &qmmm
> > > qm_theory='AM1', grms_tol=0.0002,
> > > tight_p_conv=1, scfconv=1.d-10, qmcharge=-1,
> > > /
> > > 7 N9 31.5580 25.3660 39.2430
> > > ............................
> > >
> > >
> > > Apparently you are right. I repeated the job, making sure to have
> > inserted
> > > "-m 2". Could that be fixed?
> >
> > > Although I fully agree with your warning about trying to parameterize
> > > organic radicals, I tried to have the antechamber output, on which to
> > > substitute data from the ab initio calculation, as I find it difficult
> to
> > > build the entire FF without a layout.
> >
> > For now, why not just run antechamber without the -bcc flag? That will
> > give
> > you all the files, just without the (rather incorrect) am1-bcc charges.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 18
> Date: Mon, 17 Nov 2014 23:00:41 +0530
> From: Robin Jain <robinjain.chem.gmail.com>
> Subject: Re: [AMBER] help
> To: amber <amber.ambermd.org>
> Message-ID:
> <
> CA+QHj+mnNKY+W81WChOiyCq4tnfbLmurcZODYSauu8gHO6aVxg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> My question is that my box is cubic and i want to maintain periodic
> boundary condition also then am i going in right way or not.
>
> On Thu, Nov 13, 2014 at 11:29 AM, Robin Jain <robinjain.chem.gmail.com>
> wrote:
>
> >
> > Dear all,
> > I want to simulate an organic molecule in methanol. Since i want to
> > simulate it in fix no. of methanol 80 and box size 17.58. For this i have
> > follow this process-
> >
> > first i used *AddtoBox* command to simulte my sytem with fix no. of
> > solvent and then i go to *xleap* and used *setbox* command and then i
> > used *saveamberparm* command for *prmtop* and *inpcrd* file and finally i
> > used *chbox* command to get desired box dimension in inpcrd file and then
> > i manually edit prmtop file in FLAG_BOX_DIMENSIONS.
> >
> > Now i want to know that have i done right or wrong and how could i manage
> > periodic boundary condition in that.
> > --
> > Robin Jain
> >
> >
> >
>
>
> --
> Robin Jain
>
>
> ------------------------------
>
> Message: 19
> Date: Mon, 17 Nov 2014 13:48:24 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] help
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: robinjain.chem.gmail.com
> Message-ID: <1416250104.2536.5.camel.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Did you get Dave's response? See it here:
> http://archive.ambermd.org/201411/0162.html
>
> Please make sure you are receiving emails from ambermd.org and that they
> are not being filtered.
>
> You may also consider using more informative subjects for your email to
> help would-be responders figure out quickly if they might know enough to
> help or not ("help" is not descriptive).
>
> HTH,
> Jason
>
> On Mon, 2014-11-17 at 23:00 +0530, Robin Jain wrote:
> > My question is that my box is cubic and i want to maintain periodic
> > boundary condition also then am i going in right way or not.
> >
> > On Thu, Nov 13, 2014 at 11:29 AM, Robin Jain <robinjain.chem.gmail.com>
> > wrote:
> >
> > >
> > > Dear all,
> > > I want to simulate an organic molecule in methanol. Since i want to
> > > simulate it in fix no. of methanol 80 and box size 17.58. For this i
> have
> > > follow this process-
> > >
> > > first i used *AddtoBox* command to simulte my sytem with fix no. of
> > > solvent and then i go to *xleap* and used *setbox* command and then i
> > > used *saveamberparm* command for *prmtop* and *inpcrd* file and
> finally i
> > > used *chbox* command to get desired box dimension in inpcrd file and
> then
> > > i manually edit prmtop file in FLAG_BOX_DIMENSIONS.
> > >
> > > Now i want to know that have i done right or wrong and how could i
> manage
> > > periodic boundary condition in that.
> > > --
> > > Robin Jain
> > >
> > >
> > >
> >
> >
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 20
> Date: Mon, 17 Nov 2014 11:35:24 -0800
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] GPU enabled Hardware specification
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <D08F8D5E.4CB4B%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Yes - it is known as marketing fluff!!!
>
> The stock heat sink is heavily tested and is the same approach used for
> the active Tesla cards. It is also known to work properly with multiple
> cards in a box. All the other heat sinks are just marketing people trying
> to get value add. Note, I very much doubt they test their cards to the
> types of temperatures and loads that running AMBER jobs 24/7 generate so
> I'd question their claims. The also almost certainly did not design these
> heat sinks for having 4 GPUs all next to each other in a single box. So
> feel free to buy the sexy looking heat sink cards but my advice would be
> to stick to the designs that are the closest to what the Tesla cards use.
>
> All the best
> Ross
>
>
> On 11/17/14, 1:17 AM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> wrote:
>
> >According to their documents the new heatsink design enhanced the cooling
> >performance much better than the reference design.
> >
> >Apart from its weird cooling system, GTX780-DC2-3GD5 (which is similar to
> >the reference design GTX780-3GD3), is available for me to buy. But I am
> >not sure that, this is a reliable GPU for MD or it is better to seek for
> >the GTX780-3GD3.
> >
> >On Sun, Nov 16, 2014 at 11:52 PM, Ross Walker <ross.rosswalker.co.uk>
> >wrote:
> >
> >> Hi Reza,
> >>
> >> If you want to play it safe I would suggest the last one in that list -
> >> GTX780-3GD5 - this is the reference design with NVIDIA's stock heatsink
> >>so
> >> much better tested than the rest which all have weird custom heatsinks
> >> designed to look k00l.
> >>
> >> All the best
> >> Ross
> >>
> >>
> >>
> >> On 11/15/14, 11:49 PM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com>
> >> wrote:
> >>
> >> >Dear Ross,
> >> >
> >> >Thank you very much, Is the OC make it an unknown issue?
> >> >Since RMA is not a possible option in my country, I have to be very
> >> >cautious about the GPU specification before buying it.
> >> >
> >> >So I would be very grateful if you could recommend me the appropriate
> >> >GPU(s) from the following GTX780 list?
> >> >
> >> >Here are the different editions of GTX780 which I took from Asus
> >>website:
> >> >ROG POSEIDON-GTX780-P-3GD5
> >> ><http://www.asus.com/Graphics_Cards/ROG_POSEIDONGTX780P3GD5/>
> >> >GTX780-DC2OC-3GD5 <http://www.asus.com/Graphics_Cards/GTX780DC2OC3GD5/
> >
> >> >STRIX-GTX780-OC-6GD5
> >> ><http://www.asus.com/Graphics_Cards/STRIXGTX780OC6GD5/>
> >> >ROG POSEIDON-GTX780-3GD5
> >> ><http://www.asus.com/Graphics_Cards/ROG_POSEIDONGTX7803GD5/>
> >> >GTX780-DC2-3GD5 <http://www.asus.com/Graphics_Cards/GTX780DC23GD5/>
> >> >GTX780-3GD5 <http://www.asus.com/Graphics_Cards/GTX7803GD5/>
> >> >
> >> >http://www.asus.com/Graphics_Cards/
> >> >
> >> >Regards,
> >> >
> >> >On Sun, Nov 16, 2014 at 12:19 AM, Ross Walker <ross.rosswalker.co.uk>
> >> >wrote:
> >> >
> >> >> Hi Reza,
> >> >>
> >> >> I have not tried any STRIX branded GPUs - and must admit to not
> >>actually
> >> >> knowing what it stands for. My suggestion would be to suck it and
> >>see.
> >> >> (Asus tend to be a nice brand though).
> >> >>
> >> >> Once you receive the GPU run the AMBER validation test on it:
> >> >>
> https://dl.dropboxusercontent.com/u/708185/GPU_Validation_Test.tar.gz
> >> >>
> >> >> And if all answers do not come out the same - RMA it and got for a
> >> >>regular
> >> >> clock (or these days regular OC) card.
> >> >>
> >> >> All the best
> >> >> Ross
> >> >>
> >> >>
> >> >>
> >> >> On 11/15/14, 2:41 AM, "M. Reza Ganjalikhany" <ganjalikhany.gmail.com
> >
> >> >> wrote:
> >> >>
> >> >> >How about STRIX OC edition of GTX780?
> >> >> >Is STRIX edition suitable for GPU accelerated MD?
> >> >> >
> >> >> >such as:
> >> >> >ASUS STRIX-GTX780-OC-6GD5
> >> >> >GeForce GTX 780 - 6GB - STRIX
> >> >> >
> >> >> >On Wed, Oct 29, 2014 at 12:32 AM, Ross Walker
> >><ross.rosswalker.co.uk>
> >> >> >wrote:
> >> >> >
> >> >> >> Agreed - although to caveat that - the GTX780 silicon is fairly
> >> >>mature
> >> >> >> these days and from the various hardware I have been testing the
> >> >> >> superclocked chips actually seem to be okay right now. You should
> >> >>still
> >> >> >> test it to be sure but given it is fairly mature silicon the
> >>yields
> >> >>(and
> >> >> >> thus achievable clock speeds) tend to drift upwards with time.
> >>E.g. I
> >> >> >> certainly would not entertain an overclocked GTX980 right now. But
> >> >>in a
> >> >> >> year - maybe...
> >> >> >>
> >> >> >> As for brand both Asus and EVGA tend to be pretty good brands so
> >> >>that's
> >> >> >> not a worry.
> >> >> >>
> >> >> >> All the best
> >> >> >> Ross
> >> >> >>
> >> >> >>
> >> >> >> On 10/28/14, 12:59 PM, "Scott Le Grand" <varelse2005.gmail.com>
> >> >>wrote:
> >> >> >>
> >> >> >> >Superclocked is a "super" way to get inaccurate results.
> >>Avoid...
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >On Tue, Oct 28, 2014 at 12:50 PM, M. Reza Ganjalikhany <
> >> >> >> >ganjalikhany.gmail.com> wrote:
> >> >> >> >
> >> >> >> >> Thank you very much fro your help.
> >> >> >> >>
> >> >> >> >> And the last question:
> >> >> >> >> Is there any difference between EVGA GTX 780
> >> >> >> >> <
> >> >> >> >>
> >> >> >> >>
> >> >> >>
> >> >> >>
> >> >>
> >> >>
> >>
> >>
> http://www.amazon.com/gp/product/B00CTY84KI/ref=as_li_qf_sp_asin_tl?ie=UT
> >> >> >>
> >> >>
> >>
> >>>>>>>>F8&camp=211189&creative=373489&creativeASIN=B00CTY84KI&link_code=as
> >>>>>>>>3&
> >> >>>>>>ta
> >> >> >>>>g=
> >> >> >> >>freelydownloa-20
> >> >> >> >> >
> >> >> >> >> and ASUS GTX 780 (GTX780-3GD5)
> >> >> >> >> <http://www.asus.com/Graphics_Cards/GTX7803GD5/>?
> >> >> >> >> It seems that EVGA has superclocked option while ASUS doesn't
> >> >>have.
> >> >> >> >> Does superclocked option play an important role in GPU
> >> >>performance?
> >> >> >> >>
> >> >> >> >> On Tue, Oct 28, 2014 at 6:23 PM, Ross Walker
> >> >><ross.rosswalker.co.uk>
> >> >> >> >> wrote:
> >> >> >> >>
> >> >> >> >> > 780TI is about the same speed as a Titan-Black but (in about
> >> >>70% of
> >> >> >> >> cases)
> >> >> >> >> > gives incorrect numerical answers.
> >> >> >> >> >
> >> >> >> >> > 780 on the other hand gives the correct numerical answers.
> >> >> >> >> >
> >> >> >> >> > So, my advice is to go with 780 or Titan-Black and avoid
> >>780TI.
> >> >> >> >> >
> >> >> >> >> > All the best
> >> >> >> >> > Ross
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > On 10/28/14, 2:41 AM, "M. Reza Ganjalikhany"
> >> >> >><ganjalikhany.gmail.com>
> >> >> >> >> > wrote:
> >> >> >> >> >
> >> >> >> >> > >what is the difference between GTX 780 and GTX780Ti in
> >> >> >>performance?
> >> >> >> >> > >
> >> >> >> >> > >On Tue, Oct 28, 2014 at 12:49 AM, Scott Le Grand
> >> >> >> >><varelse2005.gmail.com
> >> >> >> >> >
> >> >> >> >> > >wrote:
> >> >> >> >> > >
> >> >> >> >> > >> The successor is the Asus X99-E WS plus Core i7-5930K CPU.
> >> >> >> >> > >>
> >> >> >> >> > >>
> >> >> >> >> > >>
> >> >> >> >> > >>
> >> >> >> >> > >>
> >> >> >> >> > >> On Mon, Oct 27, 2014 at 1:39 PM, M. Reza Ganjalikhany <
> >> >> >> >> > >> ganjalikhany.gmail.com> wrote:
> >> >> >> >> > >>
> >> >> >> >> > >> > Dear Amber Developers,
> >> >> >> >> > >> >
> >> >> >> >> > >> > I decided to assemble my own PC with GPU enabled
> >>according
> >> >>to
> >> >> >> >>your
> >> >> >> >> > >> website
> >> >> >> >> > >> > recommendation.
> >> >> >> >> > >> > Due to some hardware limitations, the recommended
> >> >>Motherboard
> >> >> >> >> (P9X79-E
> >> >> >> >> > >> WS)
> >> >> >> >> > >> > is not available but other P9X79 families are available
> >> >>such
> >> >> >>as
> >> >> >> >> P9X79
> >> >> >> >> > >>WS,
> >> >> >> >> > >> > P9X79 DELUX and P9X79. Is this make the GPU simulation
> >>so
> >> >> >> >>different
> >> >> >> >> > >>if I
> >> >> >> >> > >> > use P9X79 WS instead of E WS?
> >> >> >> >> > >> > What is the main point which should be noticed?
> >> >> >> >> > >> >
> >> >> >> >> > >> > Regards,
> >> >> >> >> > >> > M.Reza
> >> >> >> >> > >> > _______________________________________________
> >> >> >> >> > >> > AMBER mailing list
> >> >> >> >> > >> > AMBER.ambermd.org
> >> >> >> >> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> > >> >
> >> >> >> >> > >> _______________________________________________
> >> >> >> >> > >> AMBER mailing list
> >> >> >> >> > >> AMBER.ambermd.org
> >> >> >> >> > >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> > >>
> >> >> >> >> > >_______________________________________________
> >> >> >> >> > >AMBER mailing list
> >> >> >> >> > >AMBER.ambermd.org
> >> >> >> >> > >http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > _______________________________________________
> >> >> >> >> > AMBER mailing list
> >> >> >> >> > AMBER.ambermd.org
> >> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> >
> >> >> >> >> _______________________________________________
> >> >> >> >> AMBER mailing list
> >> >> >> >> AMBER.ambermd.org
> >> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >>
> >> >> >> >_______________________________________________
> >> >> >> >AMBER mailing list
> >> >> >> >AMBER.ambermd.org
> >> >> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >_______________________________________________
> >> >> >AMBER mailing list
> >> >> >AMBER.ambermd.org
> >> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >_______________________________________________
> >> >AMBER mailing list
> >> >AMBER.ambermd.org
> >> >http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1041, Issue 1
> **************************************
>
--
Robin Jain
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 18 2014 - 08:00:02 PST
