I am running 331.38 on two Ubuntu machines (12.04 and 12.10) with two Titans each. Everything works fine with a slightly lower temp than before.
Best regards
> From: amber-request.ambermd.org
> Subject: AMBER Digest, Vol 749, Issue 1
> To: amber.ambermd.org
> Date: Wed, 29 Jan 2014 12:00:01 -0800
>
> 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
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>
> 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: OSX Mavericks: Failure in parallel installation of
> Amber12 (Jason Swails)
> 2. Re: amber12 GPU performance degrades? (Guanglei Cui)
> 3. Re: OSX Mavericks: Failure in parallel installation of
> Amber12 (David A Case)
> 4. Re: optimise ligand geomatry before MD (Karl Kirschner)
> 5. Re: question (. mirage)
> 6. Re: question (Jason Swails)
> 7. Prep file is empty (DEBOSTUTI GHOSHDASTIDAR)
> 8. Re: question (. mirage)
> 9. Re: Prep file is empty (David A Case)
> 10. Has anyone tested to newer nvidia drivers for linux?
> (Matthew Wampole)
> 11. Re: Has anyone tested to newer nvidia drivers for linux?
> (Ross Walker)
> 12. Re: Has anyone tested to newer nvidia drivers for linux?
> (Jan-Philip Gehrcke)
> 13. Re: AmberTools vs. Amber: Installation practice subject to
> different licenses - Solved. (Sternberg, Michael G.)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Jan 2014 15:06:52 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] OSX Mavericks: Failure in parallel installation
> of Amber12
> To: amber.ambermd.org
> Message-ID: <1390939612.21114.26.camel.heroes-out.rutgers.edu>
> Content-Type: text/plain; charset="UTF-8"
>
> On Tue, 2014-01-28 at 13:53 -0500, Robyn Ayscue wrote:
> > I've successfully compiled Amber12/AmberTools13 on my MacBookPro and I've
> > found that you must activate the root account and compile as root.
>
> I've never had to compile as root on my Mac (and I would strongly
> encourage people not to). I have built Amber on OS X 10.5 through 10.9
> without root. This sounds like an issue with file ownership or
> permissions -- you need to make sure that AMBERHOME is owned
> (recursively) by the user you are trying to install as, and that the
> files have the appropriate permissions to allow reading, writing, and
> executing:
>
> sudo chown -R <user> /path/to/amber
>
> > Logging
> > in to a shell as yourself and trying to compile by typing "sudo" in front
> > of every command doesn't seem to work well with Amber programs (even if you
> > have full admin privileges). I would always get arcane errors, like the one
> > about $AMBERHOME not being set (even when typing "echo $AMBERHOME" proved
> > that it really was set)
>
> This is a common stumbling block. AMBERHOME is in fact _not_ set when
> you see complaints about AMBERHOME not being set... the key qualifier
> being that AMBERHOME is not set in the shell being used to run the
> commands. By default, "sudo" does not necessarily inherit the calling
> shell's environment (you need to use the -E flag to do this). This is
> actually not unique to Amber, although most other programs do not rely
> so heavily on a particular environment variable as Amber does.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 28 Jan 2014 15:27:32 -0500
> From: Guanglei Cui <amber.mail.archive.gmail.com>
> Subject: Re: [AMBER] amber12 GPU performance degrades?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAOYnuV5e+PPvjjQME7c+KUEqT2Y2zTUDvkMFV_g05bT79E32yQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks Jason.
>
>
> On Tue, Jan 28, 2014 at 2:56 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
> > On Tue, 2014-01-28 at 14:21 -0500, Guanglei Cui wrote:
> > > Hi Jan-Philip and Ross,
> > >
> > > Thanks for the response. I suspect the performance drop I saw is most
> > > likely due to running 2 jobs on the same card because I didn't specify
> > > CUDA_VISIBLE_DEVICES in the first place. And, the same CUDA device ID was
> > > reported in the output files.
> > >
> > > However, setting CUDA_VISIBLE_DEVICES in the job script doesn't seem to
> > > affect the device ID reported in mdout. With the variable set to 0 and 1
> > > individually, CUDA DEVICE ID 0 is reported in both mdouts, even though
> > > nvidia-smi seems to suggest both GPUs are being used.
> >
> > Unfortunately this is expected behavior. The device number is numbered
> > from 0 to N of the N GPUs specified by CUDA_VISIBLE_DEVICES. It may
> > make sense for Amber to start printing out the value of the
> > CUDA_VISIBLE_DEVICES environment variable when it prints out device
> > number, too.
> >
> > This is part of the CUDA API itself, so Amber has no control.
> >
> > One thing to be careful of is that the device numbering in nvidia-smi
> > does _not_ necessarily match the device numbering that one gets from the
> > CUDA API. If you want to get the mapping that the CUDA API returns, you
> > need to use the "deviceQuery" program included with the CUDA SDK
> > instead.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Guanglei Cui
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 28 Jan 2014 21:39:25 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] OSX Mavericks: Failure in parallel installation
> of Amber12
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20140129023925.GD4454.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Tue, Jan 28, 2014, Robyn Ayscue wrote:
>
> > I've successfully compiled Amber12/AmberTools13 on my MacBookPro and I've
> > found that you must activate the root account and compile as root.
>
> Let me second Jason's comment: don't do this!
>
> Find the first error that arises from an installation as an ordinary user, and
> try to work from there. As Jason says, it certainly sounds like a permissions
> problem. (It could be that compilers are needing root permissions, but we'd
> need more info. If you can't figure it out, consider posting the very first
> error you get with a clean install.)
>
> Many, many Amber users run on Mac's without needing root privileges.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 29 Jan 2014 10:13:53 +0100
> From: Karl Kirschner <k.n.kirschner.gmail.com>
> Subject: Re: [AMBER] optimise ligand geomatry before MD
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAF=D-byFkMGJhe=YFnUtszAoMe7_df=ZHvCmpKCzTU+vD1NGfQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello Nitin,
>
> Yes, in general one should optimize a ligand's geometry prior to an MD
> simulation. If the force-field parameters are present and trustworthy, then
> performing an MM minimization is sufficient. This is important so that you
> do not introduce artificially large forces, arising from the molecule
> residing at a high energy state on the MM's potential energy surface, at
> the start of your simulation.
>
> However, if the parameters are not present (e.g. torsion terms, partial
> atomic charges) then you will need to optimize the ligand using QM or
> Antechamber (i.e. sqm). Most Amber force fields were developed with
> geometries optimized at HF/6-31G(d), but many use the Antechamber/sqm
> method for optimizing ligands, which I believe is semiempirical. Both
> methods are comparable, in the sense that they optimize the geometry, but
> differ in the theory used to do so. Different theories will lead to
> different optimized geometries, sometimes they have relatively minor
> differences (e.g. bond distances) and sometimes they are more significant
> (e.g. different rotamers).
>
> Once you have the optimized conformation, then you use it as an input to
> determine partial atomic charges. There is quite a bit of literature for
> this already present for Amber, including using multiple conformations to
> determine a single charge set for a molecule.
>
> It is reasonable/necessary to optimize a ligand's conformation that you
> obtained from a docking pose. If you used flexible docking methods, then
> note that this conformation may change due to the absence of the binding
> pocket.
>
> As for websites/methods that you can use, Antechamber's can perform an
> optimization (via sqm) and to determine partial atomic charges. The R.E.D.
> website will also allow you to do both in a manner that is balanced with
> the Amber force fields. You can also have the option of downloading a
> number of QM software packages, such as Gamess and Gaussian. I would
> suggest doing some more reading regarding partial atomic charge
> determination and ligand/residue model building (e.g. Parm94, Gaff,
> Glycam06, R.E.D., Wolf2Pack, etc. papers).
>
> Best regards,
> Karl
>
> On Tue, Jan 28, 2014 at 7:44 PM, Nitin Sharma <sharmanitin.nus.edu.sg>wrote:
>
> > Dear amber users,
> >
> > Is it necessary to optimize ligand geometry before molecular dynamics
> > simulation?
> >
> > I am using AMBER for MD simulation.
> >
> > I have seen studies where ligand was parameterized according to quantum
> > chemical calculations, which included performing a geometry optimization
> > with Gaussian98
> > at the Hartree-Fock/6-31G* level before determining atomic charges and
> > atomic types using Antechamber module of the Amber molecular dynamics
> > software package.
> >
> > However, i have seen studies where ligand were assigned generalized Amber
> > force field (GAFF) atom types and AM1-BCC atomic charges obtained by adding
> > the bond charge correction (BCC) using Antechamber.
> >
> > Are both protocols comparable ?
> >
> > As i am thinking to use pose generated as result of docking will the
> > ligand geometry optimization be good idea?
> >
> > can someone also tell me web-server or software to do ligand geometry
> > optimization for AMBER MD simulation
> >
> >
> > Thanks and regards,
> > Nitin Sharma
> > Department of Pharmacy,Faculty of Science,National University of
> > Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:
> > sharmanitin.nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 29 Jan 2014 12:53:28 +0000
> From: ". mirage" <m.o.m.live.fr>
> Subject: Re: [AMBER] question
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <DUB119-W44A7A9E5CDAB50A317669EB9AC0.phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi, anny help please
>
> > From: m.o.m.live.fr
> > To: amber.ambermd.org
> > Date: Mon, 27 Jan 2014 13:04:23 +0000
> > Subject: [AMBER] question
> >
> > Hi amber user'sin order to study a comlexes type hote:invited 1:1 and 2:1 by calculating mmpbsa energy I chose one type on hote molecule (H) and two types of guest (A or B). we have then H>A, H>B, H>AA and H>BB For each type of complex, the guest B has the most stable orientations (minimum deltaG), but it has also some stable orientations A than B. My question is, what we say that B is more stable than A (on comparing only the orientation which have the minimum delta G ignoring some more stable orientation A than B.Thank's in advance for all reponse.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 29 Jan 2014 08:37:08 -0500
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] question
> To: amber.ambermd.org
> Message-ID: <1391002628.24707.24.camel.heroes-out.rutgers.edu>
> Content-Type: text/plain; charset="UTF-8"
>
> On Mon, 2014-01-27 at 13:04 +0000, . mirage wrote:
> > Hi amber user'sin order to study a comlexes type hote:invited 1:1 and
> > 2:1 by calculating mmpbsa energy I chose one type on hote molecule (H)
> > and two types of guest (A or B). we have then H>A, H>B, H>AA and H>BB
> > For each type of complex, the guest B has the most stable orientations
> > (minimum deltaG), but it has also some stable orientations A than B.
> > My question is, what we say that B is more stable than A (on comparing
> > only the orientation which have the minimum delta G ignoring some more
> > stable orientation A than B.Thank's in advance for all reponse.
>
> I'm not sure I understand the question. It seems that you have a host
> that has two binding sites that can bind one of two guests; A or B. It
> seems that the host can bind with either one or two of the guests, but
> not one of each guest (i.e., not H>AB or H>BA), presumably because they
> are never mixed together, I'm not sure. You ran molecular dynamics (I
> am assuming) on these complexes and then performed MM/PBSA analyses on
> the trajectories and got energies.
>
> An important distinction: a single orientation is NOT a Delta G. Free
> energies are ensemble averages over a Boltzmann-weighted distribution.
> Simply discarding snapshots because they don't fit your expectations is
> not a good approach. If you want to make some comparison of stability,
> it is not the "lowest energy" snapshots you should be comparing, it is
> the full ensemble averages.
>
> If you have not run molecular dynamics simulations to generate the
> snapshots you used for MM/PBSA and instead used something like docking
> poses you got from some docking program then this is different. Docking
> does not generate a proper Boltzmann-weighted distribution so you can
> never be quite sure how to weight each orientation. In this case you
> may be able to make an argument to discard unfavorable poses, but
> ultimately such choices will be based on subjective evaluations and
> hand-waving.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 29 Jan 2014 19:37:14 +0530
> From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
> Subject: [AMBER] Prep file is empty
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAJYAmDXt9Et_uEBmJ6i436=YJBO2SWBeaSnrZOKHVu6xWjzFLQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> I have calculated esp charges for BF4 using gaussian G09.While converting
> the log file to the prep file using antechamber, the Fluorine atoms are not
> being recognized and NEWPDB is empty. However, there was no error shown
> while running antechamber. The log file and the corresponding mol2 file are
> fine. I have tried using the -j flag but it did not help. On using -s 2 the
> following are shown
>
> Running: /usr/local/bin/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Running: /usr/local/bin/amber12//bin/prepgen -i ANTECHAMBER_PREP.AC -f int
> -o BF4_ani.prep -rn "MOL" -rf molecule.res
>
> --
> Debostuti Ghosh Dastidar
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 29 Jan 2014 14:39:13 +0000
> From: ". mirage" <m.o.m.live.fr>
> Subject: Re: [AMBER] question
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID: <DUB119-W3B14D228069D8592FE417B9AC0.phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> HiMy work is to do molecular dynamic for each guest separately and after that to do mmpbsa over full trajectory and in final compare the result.
> the most stable orientation= the orientation which has minimum deltaG in 1:1 or in 2:1, (not the minima for one complex trajectory)
> The "most stable orientation for 1:1 complex H>B" is more stable then "the most stable orientation for 1:1 complex H>A"
> The "most stable orientation for 2:1 complex H>BB" is more stable then "the most stable orientation for 2:1 complex H>AA"
>
> But out the "most stable orientation" i have somme orientation in H>A or H>AA which are more stable of H>B or or H>BB respectively
> My question is, what we say that B is more stable than A (on comparing only the orientation which have the better delta G ignoring some more stable orientation A than B.
> Thank's in advance for all reponse.
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Date: Wed, 29 Jan 2014 08:37:08 -0500
> > Subject: Re: [AMBER] question
> >
> > On Mon, 2014-01-27 at 13:04 +0000, . mirage wrote:
> > > Hi amber user'sin order to study a comlexes type hote:invited 1:1 and
> > > 2:1 by calculating mmpbsa energy I chose one type on hote molecule (H)
> > > and two types of guest (A or B). we have then H>A, H>B, H>AA and H>BB
> > > For each type of complex, the guest B has the most stable orientations
> > > (minimum deltaG), but it has also some stable orientations A than B.
> > > My question is, what we say that B is more stable than A (on comparing
> > > only the orientation which have the minimum delta G ignoring some more
> > > stable orientation A than B.Thank's in advance for all reponse.
> >
> > I'm not sure I understand the question. It seems that you have a host
> > that has two binding sites that can bind one of two guests; A or B. It
> > seems that the host can bind with either one or two of the guests, but
> > not one of each guest (i.e., not H>AB or H>BA), presumably because they
> > are never mixed together, I'm not sure. You ran molecular dynamics (I
> > am assuming) on these complexes and then performed MM/PBSA analyses on
> > the trajectories and got energies.
> >
> > An important distinction: a single orientation is NOT a Delta G. Free
> > energies are ensemble averages over a Boltzmann-weighted distribution.
> > Simply discarding snapshots because they don't fit your expectations is
> > not a good approach. If you want to make some comparison of stability,
> > it is not the "lowest energy" snapshots you should be comparing, it is
> > the full ensemble averages.
> >
> > If you have not run molecular dynamics simulations to generate the
> > snapshots you used for MM/PBSA and instead used something like docking
> > poses you got from some docking program then this is different. Docking
> > does not generate a proper Boltzmann-weighted distribution so you can
> > never be quite sure how to weight each orientation. In this case you
> > may be able to make an argument to discard unfavorable poses, but
> > ultimately such choices will be based on subjective evaluations and
> > hand-waving.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 29 Jan 2014 10:27:40 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] Prep file is empty
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20140129152740.GB81614.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Wed, Jan 29, 2014, DEBOSTUTI GHOSHDASTIDAR wrote:
> >
> > I have calculated esp charges for BF4 using gaussian G09.While converting
> > the log file to the prep file using antechamber, the Fluorine atoms are not
> > being recognized and NEWPDB is empty.
>
> 1. Can you give the exact command-line arguments you are using?
> 2. What makes you conclude that the fluorine atoms are not being recognized?
>
> > The log file and the corresponding mol2 file are fine
>
> If the "mol2 file is fine", can you not use that? NEWPDB is just an
> intermediate file in any case. If you have the mol2 file, you should be good
> to go.
>
> I'm probably not understanding what you did, and what exactly went awry.
>
> ...dac
>
> >
> > Running: /usr/local/bin/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> > ANTECHAMBER_AC.AC -p gaff
> >
> > Running: /usr/local/bin/amber12//bin/prepgen -i ANTECHAMBER_PREP.AC -f int
> > -o BF4_ani.prep -rn "MOL" -rf molecule.res
>
> p.s. Note that antechamber doesn't know anything about boron. You'll have to
> generate parameters for that on your own (or follow the instructions in
> section 2.2 of tutorial A15.)
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 29 Jan 2014 15:43:12 +0000
> From: Matthew Wampole <Matthew.Wampole.jefferson.edu>
> Subject: [AMBER] Has anyone tested to newer nvidia drivers for linux?
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <51430d8869104b96b515db7b6d572ac2.BLUPR05MB564.namprd05.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi all,
>
> I'm looking to upgrade my nvidia drivers from 325.15 to 331.38 and was wondering if anyone has tested ambers stability on newer cards (specifically I use a GTX680 and TITANS) with this new driver. Thanks.
>
> Matt
>
> The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
>
> CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.
>
>
>
> ------------------------------
>
> Message: 11
> Date: Wed, 29 Jan 2014 08:28:33 -0800
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] Has anyone tested to newer nvidia drivers for
> linux?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <CF0E6B03.387A1%ross.rosswalker.co.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Hi Matt,
>
> The 331.20 driver works great with 780 and titan. I have not yet tried the
> 331.38 driver but there is no reason to think it would regress any of the
> Titan / 780 fixes.
>
> All the best
> Ross
>
>
>
> On 1/29/14, 7:43 AM, "Matthew Wampole" <Matthew.Wampole.jefferson.edu>
> wrote:
>
> >Hi all,
> >
> >I'm looking to upgrade my nvidia drivers from 325.15 to 331.38 and was
> >wondering if anyone has tested ambers stability on newer cards
> >(specifically I use a GTX680 and TITANS) with this new driver. Thanks.
> >
> >Matt
> >
> >The information contained in this transmission contains privileged and
> >confidential information. It is intended only for the use of the person
> >named above. If you are not the intended recipient, you are hereby
> >notified that any review, dissemination, distribution or duplication of
> >this communication is strictly prohibited. If you are not the intended
> >recipient, please contact the sender by reply email and destroy all
> >copies of the original message.
> >
> >CAUTION: Intended recipients should NOT use email communication for
> >emergent or urgent health care matters.
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Wed, 29 Jan 2014 17:45:14 +0100
> From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
> Subject: Re: [AMBER] Has anyone tested to newer nvidia drivers for
> linux?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <52E9301A.8060805.googlemail.com>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> We have a machine with four 780s. With the 325.15 driver, the kernel
> would regularly report unresponsive GPUs. Update to 331.20 fixed this
> mean issue for us. Go ahead, I would say :)
>
> On 01/29/2014 05:28 PM, Ross Walker wrote:
> > Hi Matt,
> >
> > The 331.20 driver works great with 780 and titan. I have not yet tried the
> > 331.38 driver but there is no reason to think it would regress any of the
> > Titan / 780 fixes.
> >
> > All the best
> > Ross
> >
> >
> >
> > On 1/29/14, 7:43 AM, "Matthew Wampole" <Matthew.Wampole.jefferson.edu>
> > wrote:
> >
> >> Hi all,
> >>
> >> I'm looking to upgrade my nvidia drivers from 325.15 to 331.38 and was
> >> wondering if anyone has tested ambers stability on newer cards
> >> (specifically I use a GTX680 and TITANS) with this new driver. Thanks.
> >>
> >> Matt
> >>
> >> The information contained in this transmission contains privileged and
> >> confidential information. It is intended only for the use of the person
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> ------------------------------
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> Message: 13
> Date: Wed, 29 Jan 2014 19:36:54 +0000
> From: "Sternberg, Michael G." <sternberg.anl.gov>
> Subject: Re: [AMBER] AmberTools vs. Amber: Installation practice
> subject to different licenses - Solved.
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <48E9869F-8EEA-40E5-B4AA-C6CABA289FA7.anl.gov>
> Content-Type: text/plain; charset="us-ascii"
>
> Jason, all,
>
> Thank you for the reminder - you are correct about point 3 in the license. >From the lack of other responses I take it that this is not a pressing issue. I was asking because sensibilities were raised by the terms of several commercial vendors, both related and unrelated to materials modeling.
>
> That said, on review, I noticed the -noamber configure option (new in AmberTools-12), and I was able to use that to indeed make two builds with minimal fuss from a single build script. Users will load one of two mutually exclusive environment modules to get access, each setting AMBERHOME appropriately, with the "amber" directory being group-restricted, and "ambertools" not.
>
>
> With best regards,
> Michael
>
>
> On Jan 23, 2014, at 5:46 , Jason Swails <jason.swails.gmail.com> wrote:
> > On Wed, Jan 22, 2014 at 6:46 PM, Sternberg, Michael G. <sternberg.anl.gov>wrote:
> >>
> >> I envision having to install AmberTools twice, once standalone,
> >> world-accessible, and again in another directory as part of Amber,
> >> accessible only to a specific UNIX group.
> >
> >
> > Oooh, Gaussian :) (only without the GPL part)
> >
> >
> >> I'd love to be proven wrong on this because maintaining two installs seems
> >> like a recipe for confusion at best, requiring duplicate build scripts and
> >> patch management. I looked at the FAQ page
> >> http://ambermd.org/questions.html but it's rather ancient and has no
> >> specifics on installation.
> >>
> >
> > If your HPC has a license for Amber, then you can make it available to all
> > of your users (if you have for-profit users, like pharma employees, they
> > may need their own license).
> >
> > See point 3 at the bottom of here: http://ambermd.org/amber12.license.html,
> > which should cover you.
> >
> > In short, I've never seen a supercomputer center install and support
> > separate versions for licensing issues.
> >
> > HTH,
> > Jason
>
>
>
>
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> End of AMBER Digest, Vol 749, Issue 1
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Received on Wed Jan 29 2014 - 12:30:02 PST
