Hi,
Those plots are actually "free energy" plots obtained from bin
populations of the 2-dimensional histograms obtained from binning PC
projections 1 and 2 using the formula:
dGi = -kB * T * ln( Ni / N0 )
where dGi is the "free energy" value of bin i, kB is Boltzmann's
constant in kcal/mol*K, T is temperature in K, Ni is the population of
bin i, and N0 is the population of the most populated bin (giving the
most populated bin a free energy value of 0.0 kcal/mol). Note that I
keep putting "free energy" in quotes because unless you are reasonably
sure your bin populations have converged quite close to their
Boltzmann-weighted values, you aren't really calculating free energy,
just a weighted histogram (which may also be useful but the
nomenclature is important).
You can actually use cpptraj to construct this kind of "free energy"
histogram directly with the following input. This assumes that the
file 'pca12-ca' contains PC projection 1 in column 2 and projection 2
in column 3 and that your simulations were conducted at 300 K:
readdata pca12-ca
runanalysis hist pca12-ca:2 pca12-ca:3 free 300 out fhist.gnu bins 400
The file fhist.gnu will contain gnuplot-readable output (based on the
filename extension).
Hope this helps,
-Dan
PS - As always, make sure you're using the most up-to-date version of
cpptraj (14.22).
On Thu, Jan 1, 2015 at 3:46 PM, 汪盛 <shengwang.hust.edu.cn> wrote:
> Hi,
> I want to use aMD to my protein, but I want to know how to plot the TWO PCA vector projections on the trjactroty, like the plots of section3 of tutorial of Advanced 22 of amber.
> Especially, the 3rd Dimension looks like potential energy, whose values above zero. Apparently, those are difference of energy. What are those energy values from, Etot or deltV?
> In addition, the two PCA Vectors can be from .N or @C or combination of them?
>
> Thanks
>
>
>> -----原始邮件-----
>> 发件人: amber-request.ambermd.org
>> 发送时间: 2015年1月1日 星期四
>> 收件人: amber.ambermd.org
>> 抄送:
>> 主题: AMBER Digest, Vol 1085, Issue 1
>>
>> 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: amber14 CUDA GPU for workstation? (Ross Walker)
>> 2. Re: rms fit (Sylvester Tumusiime)
>> 3. Re: amber14 CUDA GPU for workstation? (Michael Shokhen)
>> 4. Re: amber14 CUDA GPU for workstation? (Adrian Roitberg)
>> 5. Re: amber14 CUDA GPU for workstation? (Michael Shokhen)
>> 6. Re: amber14 CUDA GPU for workstation? (Ross Walker)
>> 7. Re: Peter Kollman lectureship, Jan 8 (David A Case)
>> 8. Re: amber14 CUDA GPU for workstation? (Jason Swails)
>> 9. Re: Need help in SMD (Jason Swails)
>> 10. Re: WHAM tolerance (Jason Swails)
>> 11. Need help in Targeted MD (Pallavi Mohanty)
>> 12. Re: Need help in SMD (Kshatresh Dutta Dubey)
>> 13. Re: Need help in Targeted MD (David A Case)
>> 14. Re: Need help in Targeted MD (Carlos Simmerling)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 30 Dec 2014 12:11:42 -0800
>> From: Ross Walker <ross.rosswalker.co.uk>
>> Subject: Re: [AMBER] amber14 CUDA GPU for workstation?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <D0C846C3.4EBC9%ross.rosswalker.co.uk>
>> Content-Type: text/plain; charset="US-ASCII"
>>
>> Hi Michael,
>>
>> AmberTools does not have any programs that utilize GPUs. Do you have a
>> full copy of AMBER 14 or just AmberTools since the error message implies
>> the later?
>>
>> All the best
>> Ross
>>
>>
>> On 12/30/14, 11:31 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il> wrote:
>>
>> >Hello,
>> >
>> >I am a new Amber user.
>> >I have succeeded with installation of amber14 regular variant,
>> >but unfortunately failed to install amber14 with GPU CUDA.
>> >I would appreciate if somebody can send me a set of commands
>> >relevant for amber14 with GPU CUDA installation on my Linux workstation.
>> >
>> >Thank you,
>> >Michael
>> >
>> >See below the details about my workstation,
>> >and system report about failed installation
>> >
>> >I have received an error message
>> >after running the commands:
>> >
>> >./config -cuda gnu
>> >make install
>> >
>> >
>> >
>> >shokhen.quant-lnx:~/amber14$ make install
>> >cd AmberTools/src && make install
>> >make[1]: Entering directory `/home/shokhen/amber14/AmberTools/src'
>> >AmberTools14 has no CUDA-enabled components
>> >(cd ../../src && make cuda )
>> >make[2]: Entering directory `/home/shokhen/amber14/src'
>> >make[2]: *** No rule to make target `cuda'. Stop.
>> >make[2]: Leaving directory `/home/shokhen/amber14/src'
>> >make[1]: [cuda] Error 2 (ignored)
>> >make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> >==============================================================
>> >/home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> >This is expected if you do not have Amber14.
>> >==============================================================
>> >
>> >*****************************
>> >Michael Shokhen, PhD
>> >Associate Professor
>> >Department of Chemistry
>> >Bar Ilan University,
>> >Ramat Gan, 52900
>> >Israel
>> >email: michael.shokhen.gmail.com
>> >email: shokhen.mail.biu.ac.il
>> >_______________________________________________
>> >AMBER mailing list
>> >AMBER.ambermd.org
>> >http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 30 Dec 2014 20:33:44 +0000
>> From: Sylvester Tumusiime <stumusii.uno.edu>
>> Subject: Re: [AMBER] rms fit
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <95CAE6B6-12F5-4252-AC2B-3C548F87C626.uno.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi Dac,
>>
>> Thank you for your help in this issue.
>>
>> Silver
>>
>>
>>
>> > On Dec 29, 2014, at 8:23 PM, David A Case <case.biomaps.rutgers.edu> wrote:
>> >
>> >> On Mon, Dec 29, 2014, Sylvester Tumusiime wrote:
>> >>
>> >> I have a question regarding the use of rms fitting prior to performing
>> >> analyses like dihedral, atomicfluct and correlation.
>> >> I read in the amber tutorial 1:
>> >> /[1]http://ambermd.org/tutorials/analysis/tutorial1/
>> >> that "by default CPPTRAJ calculates the best-fit RMSD, which means each
>> >> structure is rotated and translated so as to minimize the RMSD to the
>> >> reference structure (in this case the first frame). As such, the 'rms'
>> >> command modifies coordinates for all subsequent commands unless 'nofit' is
>> >> specified"
>> >> therefore, if i am performing analysis using cpptraj, is it not necessary to
>> >> add the rms line. e.g.:
>> >> rms ToFirst :1-13&!.H= first out rmsd1.agr mass
>> >> prior to analysis since the co-ordinates will be modified again?
>> >
>> > I'm not sure what Dan (the tutorial author) meant by the term "by default"
>> > here: cpptraj only does an rms fit (and changes the coordinates) if you
>> > have an "rms line" in your script. So, yes, you (generally) need such
>> > a line for actions like atomicfluct and time correlation measurements.
>> >
>> > (Dihedrals don't change when the molecule is rotated or translated, so
>> > there it doesn't matter whether you have an rms command or not.)
>> >
>> > Thanks for asking the question: we'll update the tutorial to make this
>> > clearer.
>> >
>> > ....dac
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 30 Dec 2014 22:51:48 +0200
>> From: Michael Shokhen <michael.shokhen.biu.ac.il>
>> Subject: Re: [AMBER] amber14 CUDA GPU for workstation?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAMyFEY5daQN2-4_vAxCXOsAk1EBRhuBbE7Ro4r6hkKM6H2qPxw.mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Dear Ross,
>>
>> You are expert in AMBER.
>> In contrast, as I wrote in my previous email I am a new AMBER user.
>> I read in AMBER14 website that it includes full GPU support in PMEMD.
>> I need to install PMEMD on my linux ubuntu workstation (see details in my
>> previous
>> email). Unfortunately, I didn't find any relevant protocol in AMBER14 User
>> Gide,
>> neither in the AMBER website for the PMEMD installation at a workstation.
>> I would appreciate your help in such protocol.
>>
>> Many thanks,
>> Michael
>>
>>
>> *****************************
>> Michael Shokhen, PhD
>> Associate Professor
>> Department of Chemistry
>> Bar Ilan University,
>> Ramat Gan, 52900
>> Israel
>> email: michael.shokhen.gmail.com
>> email: shokhen.mail.biu.ac.il
>>
>>
>> On Tue, Dec 30, 2014 at 10:11 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>> >
>> > Hi Michael,
>> >
>> > AmberTools does not have any programs that utilize GPUs. Do you have a
>> > full copy of AMBER 14 or just AmberTools since the error message implies
>> > the later?
>> >
>> > All the best
>> > Ross
>> >
>> >
>> > On 12/30/14, 11:31 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
>> > wrote:
>> >
>> > >Hello,
>> > >
>> > >I am a new Amber user.
>> > >I have succeeded with installation of amber14 regular variant,
>> > >but unfortunately failed to install amber14 with GPU CUDA.
>> > >I would appreciate if somebody can send me a set of commands
>> > >relevant for amber14 with GPU CUDA installation on my Linux workstation.
>> > >
>> > >Thank you,
>> > >Michael
>> > >
>> > >See below the details about my workstation,
>> > >and system report about failed installation
>> > >
>> > >I have received an error message
>> > >after running the commands:
>> > >
>> > >./config -cuda gnu
>> > >make install
>> > >
>> > >
>> > >
>> > >shokhen.quant-lnx:~/amber14$ make install
>> > >cd AmberTools/src && make install
>> > >make[1]: Entering directory `/home/shokhen/amber14/AmberTools/src'
>> > >AmberTools14 has no CUDA-enabled components
>> > >(cd ../../src && make cuda )
>> > >make[2]: Entering directory `/home/shokhen/amber14/src'
>> > >make[2]: *** No rule to make target `cuda'. Stop.
>> > >make[2]: Leaving directory `/home/shokhen/amber14/src'
>> > >make[1]: [cuda] Error 2 (ignored)
>> > >make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> > >==============================================================
>> > >/home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> > >This is expected if you do not have Amber14.
>> > >==============================================================
>> > >
>> > >*****************************
>> > >Michael Shokhen, PhD
>> > >Associate Professor
>> > >Department of Chemistry
>> > >Bar Ilan University,
>> > >Ramat Gan, 52900
>> > >Israel
>> > >email: michael.shokhen.gmail.com
>> > >email: shokhen.mail.biu.ac.il
>> > >_______________________________________________
>> > >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: 4
>> Date: Tue, 30 Dec 2014 15:56:31 -0500
>> From: Adrian Roitberg <roitberg.ufl.edu>
>> Subject: Re: [AMBER] amber14 CUDA GPU for workstation?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <54A3117F.5050806.ufl.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> Michael
>>
>> Try looking at
>> http://jswails.wikidot.com/installing-amber14-and-ambertools14
>>
>> It has really good instructions for installation.
>>
>> Now, one question that Ross asked is important. Do you have a license
>> for amber14? Basically, did you buy it?
>>
>> Ambertools is free now, and you can download it from the amber web site.
>> Amber14 itself requires license. Ross asked his question because the
>> error you got when installing it what one should expect if amber14 is
>> not present anywhere.
>>
>> Adrian
>>
>> On 12/30/14 3:51 PM, Michael Shokhen wrote:
>> > Dear Ross,
>> >
>> > You are expert in AMBER.
>> > In contrast, as I wrote in my previous email I am a new AMBER user.
>> > I read in AMBER14 website that it includes full GPU support in PMEMD.
>> > I need to install PMEMD on my linux ubuntu workstation (see details in my
>> > previous
>> > email). Unfortunately, I didn't find any relevant protocol in AMBER14 User
>> > Gide,
>> > neither in the AMBER website for the PMEMD installation at a workstation.
>> > I would appreciate your help in such protocol.
>> >
>> > Many thanks,
>> > Michael
>> >
>> >
>> > *****************************
>> > Michael Shokhen, PhD
>> > Associate Professor
>> > Department of Chemistry
>> > Bar Ilan University,
>> > Ramat Gan, 52900
>> > Israel
>> > email: michael.shokhen.gmail.com
>> > email: shokhen.mail.biu.ac.il
>> >
>> >
>> > On Tue, Dec 30, 2014 at 10:11 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>> >> Hi Michael,
>> >>
>> >> AmberTools does not have any programs that utilize GPUs. Do you have a
>> >> full copy of AMBER 14 or just AmberTools since the error message implies
>> >> the later?
>> >>
>> >> All the best
>> >> Ross
>> >>
>> >>
>> >> On 12/30/14, 11:31 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
>> >> wrote:
>> >>
>> >>> Hello,
>> >>>
>> >>> I am a new Amber user.
>> >>> I have succeeded with installation of amber14 regular variant,
>> >>> but unfortunately failed to install amber14 with GPU CUDA.
>> >>> I would appreciate if somebody can send me a set of commands
>> >>> relevant for amber14 with GPU CUDA installation on my Linux workstation.
>> >>>
>> >>> Thank you,
>> >>> Michael
>> >>>
>> >>> See below the details about my workstation,
>> >>> and system report about failed installation
>> >>>
>> >>> I have received an error message
>> >>> after running the commands:
>> >>>
>> >>> ./config -cuda gnu
>> >>> make install
>> >>>
>> >>>
>> >>>
>> >>> shokhen.quant-lnx:~/amber14$ make install
>> >>> cd AmberTools/src && make install
>> >>> make[1]: Entering directory `/home/shokhen/amber14/AmberTools/src'
>> >>> AmberTools14 has no CUDA-enabled components
>> >>> (cd ../../src && make cuda )
>> >>> make[2]: Entering directory `/home/shokhen/amber14/src'
>> >>> make[2]: *** No rule to make target `cuda'. Stop.
>> >>> make[2]: Leaving directory `/home/shokhen/amber14/src'
>> >>> make[1]: [cuda] Error 2 (ignored)
>> >>> make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> >>> ==============================================================
>> >>> /home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> >>> This is expected if you do not have Amber14.
>> >>> ==============================================================
>> >>>
>> >>> *****************************
>> >>> Michael Shokhen, PhD
>> >>> Associate Professor
>> >>> Department of Chemistry
>> >>> Bar Ilan University,
>> >>> Ramat Gan, 52900
>> >>> Israel
>> >>> email: michael.shokhen.gmail.com
>> >>> email: shokhen.mail.biu.ac.il
>> >>> _______________________________________________
>> >>> 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
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 30 Dec 2014 23:49:24 +0200
>> From: Michael Shokhen <michael.shokhen.biu.ac.il>
>> Subject: Re: [AMBER] amber14 CUDA GPU for workstation?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAMyFEY5Mnyo9ZW_VPGmAsROjZy9-4bH5zrSGCqwV-_pXLu+viw.mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Dear Adrian,
>>
>> Yes our university group has academic license for amber14,
>> so I have both amber14 and amber tools.
>> The details about my workstation:
>>
>> cpu:Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz
>> gpu: GeForce GTX TITAN
>> cuda: version 6.0
>>
>> linux:
>>
>> Ubuntu 14.04.1 LTS
>> Release: 14.04
>> Codename: trusty
>>
>> The problem is that I used the commands for amber14 GPU installation
>> the same as you have suggested but
>> I have received an error message
>> after running the commands:
>>
>> ./config -cuda gnu
>> make install
>>
>>
>>
>> shokhen.quant-lnx:~/amber14$ make install
>> cd AmberTools/src && make install
>> make[1]: Entering directory `/home/shokhen/amber14/
>> AmberTools/src'
>> AmberTools14 has no CUDA-enabled components
>> (cd ../../src && make cuda )
>> make[2]: Entering directory `/home/shokhen/amber14/src'
>> make[2]: *** No rule to make target `cuda'. Stop.
>> make[2]: Leaving directory `/home/shokhen/amber14/src'
>> make[1]: [cuda] Error 2 (ignored)
>> make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> ==============================================================
>> /home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> This is expected if you do not have Amber14.
>> ==============================================================
>>
>> All the best,
>> Michael
>>
>>
>>
>>
>> *****************************
>> Michael Shokhen, PhD
>> Associate Professor
>> Department of Chemistry
>> Bar Ilan University,
>> Ramat Gan, 52900
>> Israel
>> email: michael.shokhen.gmail.com
>> email: shokhen.mail.biu.ac.il
>>
>>
>> On Tue, Dec 30, 2014 at 10:56 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>>
>> > Michael
>> >
>> > Try looking at
>> > http://jswails.wikidot.com/installing-amber14-and-ambertools14
>> >
>> > It has really good instructions for installation.
>> >
>> > Now, one question that Ross asked is important. Do you have a license
>> > for amber14? Basically, did you buy it?
>> >
>> > Ambertools is free now, and you can download it from the amber web site.
>> > Amber14 itself requires license. Ross asked his question because the
>> > error you got when installing it what one should expect if amber14 is
>> > not present anywhere.
>> >
>> > Adrian
>> >
>> > On 12/30/14 3:51 PM, Michael Shokhen wrote:
>> > > Dear Ross,
>> > >
>> > > You are expert in AMBER.
>> > > In contrast, as I wrote in my previous email I am a new AMBER user.
>> > > I read in AMBER14 website that it includes full GPU support in PMEMD.
>> > > I need to install PMEMD on my linux ubuntu workstation (see details in my
>> > > previous
>> > > email). Unfortunately, I didn't find any relevant protocol in AMBER14
>> > User
>> > > Gide,
>> > > neither in the AMBER website for the PMEMD installation at a workstation.
>> > > I would appreciate your help in such protocol.
>> > >
>> > > Many thanks,
>> > > Michael
>> > >
>> > >
>> > > *****************************
>> > > Michael Shokhen, PhD
>> > > Associate Professor
>> > > Department of Chemistry
>> > > Bar Ilan University,
>> > > Ramat Gan, 52900
>> > > Israel
>> > > email: michael.shokhen.gmail.com
>> > > email: shokhen.mail.biu.ac.il
>> > >
>> > >
>> > > On Tue, Dec 30, 2014 at 10:11 PM, Ross Walker <ross.rosswalker.co.uk>
>> > wrote:
>> > >> Hi Michael,
>> > >>
>> > >> AmberTools does not have any programs that utilize GPUs. Do you have a
>> > >> full copy of AMBER 14 or just AmberTools since the error message implies
>> > >> the later?
>> > >>
>> > >> All the best
>> > >> Ross
>> > >>
>> > >>
>> > >> On 12/30/14, 11:31 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
>> > >> wrote:
>> > >>
>> > >>> Hello,
>> > >>>
>> > >>> I am a new Amber user.
>> > >>> I have succeeded with installation of amber14 regular variant,
>> > >>> but unfortunately failed to install amber14 with GPU CUDA.
>> > >>> I would appreciate if somebody can send me a set of commands
>> > >>> relevant for amber14 with GPU CUDA installation on my Linux
>> > workstation.
>> > >>>
>> > >>> Thank you,
>> > >>> Michael
>> > >>>
>> > >>> See below the details about my workstation,
>> > >>> and system report about failed installation
>> > >>>
>> > >>> I have received an error message
>> > >>> after running the commands:
>> > >>>
>> > >>> ./config -cuda gnu
>> > >>> make install
>> > >>>
>> > >>>
>> > >>>
>> > >>> shokhen.quant-lnx:~/amber14$ make install
>> > >>> cd AmberTools/src && make install
>> > >>> make[1]: Entering directory `/home/shokhen/amber14/AmberTools/src'
>> > >>> AmberTools14 has no CUDA-enabled components
>> > >>> (cd ../../src && make cuda )
>> > >>> make[2]: Entering directory `/home/shokhen/amber14/src'
>> > >>> make[2]: *** No rule to make target `cuda'. Stop.
>> > >>> make[2]: Leaving directory `/home/shokhen/amber14/src'
>> > >>> make[1]: [cuda] Error 2 (ignored)
>> > >>> make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> > >>> ==============================================================
>> > >>> /home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> > >>> This is expected if you do not have Amber14.
>> > >>> ==============================================================
>> > >>>
>> > >>> *****************************
>> > >>> Michael Shokhen, PhD
>> > >>> Associate Professor
>> > >>> Department of Chemistry
>> > >>> Bar Ilan University,
>> > >>> Ramat Gan, 52900
>> > >>> Israel
>> > >>> email: michael.shokhen.gmail.com
>> > >>> email: shokhen.mail.biu.ac.il
>> > >>> _______________________________________________
>> > >>> 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
>> >
>> > --
>> > Dr. Adrian E. Roitberg
>> > Professor.
>> > Department of Chemistry
>> > University of Florida
>> > roitberg.ufl.edu
>> > 352-392-6972
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Tue, 30 Dec 2014 14:03:19 -0800
>> From: Ross Walker <ross.rosswalker.co.uk>
>> Subject: Re: [AMBER] amber14 CUDA GPU for workstation?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <D0C85FE8.4EC03%ross.rosswalker.co.uk>
>> Content-Type: text/plain; charset="US-ASCII"
>>
>> Hi Michael,
>>
>> This error means that the files required for AMBER 14 are not in your
>> AMBERHOME directory. I suspect that only the AmberTools14.tar.bz2 file was
>> extracted prior to commencing the installation. For simplicity I would
>> start again from the beginning with:
>>
>> cd $AMBERHOME
>> cd ../
>> rm -rf amber14
>> tar xvjf AmberTools14.tar.bz2
>> tar xvjf Amber14.tar.bz2 (be sure to do both of these untar commands)
>> cd amber14
>> ./configure gnu (say yes to the updates)
>> make install
>> make test (optional)
>>
>> make clean
>> ./configure -mpi gnu
>> make install
>> export DO_PARALLEL='mpirun -np 2' (or whatever syntax your mpi uses)
>> make test (optional)
>>
>> make clean
>> unset $DO_PARALLEL
>> ./configure -cuda gnu
>> make install
>> make test (optional)
>> make clean
>> ./configure -cuda -mpi gnu (only needed if you want to run across 2 GPUs
>> in a single job at the same time).
>> make install
>> export DO_PARALLEL='mpirun -np 2' (or whatever syntax your mpi uses)
>> make test (optional)
>> make clean
>> unset $DO_PARALLEL
>>
>>
>> Good luck,
>>
>> All the best
>> Ross
>>
>>
>>
>>
>>
>> On 12/30/14, 1:49 PM, "Michael Shokhen" <michael.shokhen.biu.ac.il> wrote:
>>
>> >Dear Adrian,
>> >
>> >Yes our university group has academic license for amber14,
>> >so I have both amber14 and amber tools.
>> >The details about my workstation:
>> >
>> >cpu:Intel(R) Core(TM) i7-3820 CPU . 3.60GHz
>> >gpu: GeForce GTX TITAN
>> >cuda: version 6.0
>> >
>> >linux:
>> >
>> > Ubuntu 14.04.1 LTS
>> >Release: 14.04
>> >Codename: trusty
>> >
>> >The problem is that I used the commands for amber14 GPU installation
>> >the same as you have suggested but
>> >I have received an error message
>> >after running the commands:
>> >
>> >./config -cuda gnu
>> >make install
>> >
>> >
>> >
>> >shokhen.quant-lnx:~/amber14$ make install
>> >cd AmberTools/src && make install
>> >make[1]: Entering directory `/home/shokhen/amber14/
>> >AmberTools/src'
>> >AmberTools14 has no CUDA-enabled components
>> >(cd ../../src && make cuda )
>> >make[2]: Entering directory `/home/shokhen/amber14/src'
>> >make[2]: *** No rule to make target `cuda'. Stop.
>> >make[2]: Leaving directory `/home/shokhen/amber14/src'
>> >make[1]: [cuda] Error 2 (ignored)
>> >make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> >==============================================================
>> >/home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> >This is expected if you do not have Amber14.
>> >==============================================================
>> >
>> >All the best,
>> >Michael
>> >
>> >
>> >
>> >
>> >*****************************
>> >Michael Shokhen, PhD
>> >Associate Professor
>> >Department of Chemistry
>> >Bar Ilan University,
>> >Ramat Gan, 52900
>> >Israel
>> >email: michael.shokhen.gmail.com
>> >email: shokhen.mail.biu.ac.il
>> >
>> >
>> >On Tue, Dec 30, 2014 at 10:56 PM, Adrian Roitberg <roitberg.ufl.edu>
>> >wrote:
>> >
>> >> Michael
>> >>
>> >> Try looking at
>> >> http://jswails.wikidot.com/installing-amber14-and-ambertools14
>> >>
>> >> It has really good instructions for installation.
>> >>
>> >> Now, one question that Ross asked is important. Do you have a license
>> >> for amber14? Basically, did you buy it?
>> >>
>> >> Ambertools is free now, and you can download it from the amber web site.
>> >> Amber14 itself requires license. Ross asked his question because the
>> >> error you got when installing it what one should expect if amber14 is
>> >> not present anywhere.
>> >>
>> >> Adrian
>> >>
>> >> On 12/30/14 3:51 PM, Michael Shokhen wrote:
>> >> > Dear Ross,
>> >> >
>> >> > You are expert in AMBER.
>> >> > In contrast, as I wrote in my previous email I am a new AMBER user.
>> >> > I read in AMBER14 website that it includes full GPU support in PMEMD.
>> >> > I need to install PMEMD on my linux ubuntu workstation (see details
>> >>in my
>> >> > previous
>> >> > email). Unfortunately, I didn't find any relevant protocol in AMBER14
>> >> User
>> >> > Gide,
>> >> > neither in the AMBER website for the PMEMD installation at a
>> >>workstation.
>> >> > I would appreciate your help in such protocol.
>> >> >
>> >> > Many thanks,
>> >> > Michael
>> >> >
>> >> >
>> >> > *****************************
>> >> > Michael Shokhen, PhD
>> >> > Associate Professor
>> >> > Department of Chemistry
>> >> > Bar Ilan University,
>> >> > Ramat Gan, 52900
>> >> > Israel
>> >> > email: michael.shokhen.gmail.com
>> >> > email: shokhen.mail.biu.ac.il
>> >> >
>> >> >
>> >> > On Tue, Dec 30, 2014 at 10:11 PM, Ross Walker <ross.rosswalker.co.uk>
>> >> wrote:
>> >> >> Hi Michael,
>> >> >>
>> >> >> AmberTools does not have any programs that utilize GPUs. Do you have
>> >>a
>> >> >> full copy of AMBER 14 or just AmberTools since the error message
>> >>implies
>> >> >> the later?
>> >> >>
>> >> >> All the best
>> >> >> Ross
>> >> >>
>> >> >>
>> >> >> On 12/30/14, 11:31 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
>> >> >> wrote:
>> >> >>
>> >> >>> Hello,
>> >> >>>
>> >> >>> I am a new Amber user.
>> >> >>> I have succeeded with installation of amber14 regular variant,
>> >> >>> but unfortunately failed to install amber14 with GPU CUDA.
>> >> >>> I would appreciate if somebody can send me a set of commands
>> >> >>> relevant for amber14 with GPU CUDA installation on my Linux
>> >> workstation.
>> >> >>>
>> >> >>> Thank you,
>> >> >>> Michael
>> >> >>>
>> >> >>> See below the details about my workstation,
>> >> >>> and system report about failed installation
>> >> >>>
>> >> >>> I have received an error message
>> >> >>> after running the commands:
>> >> >>>
>> >> >>> ./config -cuda gnu
>> >> >>> make install
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> shokhen.quant-lnx:~/amber14$ make install
>> >> >>> cd AmberTools/src && make install
>> >> >>> make[1]: Entering directory `/home/shokhen/amber14/AmberTools/src'
>> >> >>> AmberTools14 has no CUDA-enabled components
>> >> >>> (cd ../../src && make cuda )
>> >> >>> make[2]: Entering directory `/home/shokhen/amber14/src'
>> >> >>> make[2]: *** No rule to make target `cuda'. Stop.
>> >> >>> make[2]: Leaving directory `/home/shokhen/amber14/src'
>> >> >>> make[1]: [cuda] Error 2 (ignored)
>> >> >>> make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> >> >>> ==============================================================
>> >> >>> /home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> >> >>> This is expected if you do not have Amber14.
>> >> >>> ==============================================================
>> >> >>>
>> >> >>> *****************************
>> >> >>> Michael Shokhen, PhD
>> >> >>> Associate Professor
>> >> >>> Department of Chemistry
>> >> >>> Bar Ilan University,
>> >> >>> Ramat Gan, 52900
>> >> >>> Israel
>> >> >>> email: michael.shokhen.gmail.com
>> >> >>> email: shokhen.mail.biu.ac.il
>> >> >>> _______________________________________________
>> >> >>> 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
>> >>
>> >> --
>> >> Dr. Adrian E. Roitberg
>> >> Professor.
>> >> Department of Chemistry
>> >> University of Florida
>> >> roitberg.ufl.edu
>> >> 352-392-6972
>> >>
>> >>
>> >> _______________________________________________
>> >> 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: 7
>> Date: Tue, 30 Dec 2014 17:29:33 -0500
>> From: David A Case <case.biomaps.rutgers.edu>
>> Subject: Re: [AMBER] Peter Kollman lectureship, Jan 8
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20141230222933.GA56884.biomaps.rutgers.edu>
>> Content-Type: text/plain; charset=utf-8
>>
>> On Tue, Dec 30, 2014, Gustavo Seabra wrote:
>>
>> > The link doesn?t seem to work (for me at least). I get a message
>> > saying that "There are no presentations in the selected folder.?
>>
>> I'm guessing you have to wait until Jan 8: the lecture hasn't even taken
>> place yet....
>>
>> ....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Tue, 30 Dec 2014 17:55:33 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] amber14 CUDA GPU for workstation?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3qdmNwcU5CeBHSWz0LyUgyxZaJU3DzuqYqifYD=0_vbdA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Tue, Dec 30, 2014 at 5:03 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>>
>> > Hi Michael,
>> >
>> > This error means that the files required for AMBER 14 are not in your
>> > AMBERHOME directory. I suspect that only the AmberTools14.tar.bz2 file was
>> > extracted prior to commencing the installation. For simplicity I would
>> > start again from the beginning with:
>> >
>> > cd $AMBERHOME
>> > cd ../
>> > rm -rf amber14
>> > tar xvjf AmberTools14.tar.bz2
>> > tar xvjf Amber14.tar.bz2 (be sure to do both of these untar commands)
>> > cd amber14
>> > ./configure gnu (say yes to the updates)
>> > make install
>> > make test (optional)
>> >
>> > make clean
>> > ./configure -mpi gnu
>> > make install
>> > export DO_PARALLEL='mpirun -np 2' (or whatever syntax your mpi uses)
>> > make test (optional)
>> >
>> > make clean
>> > unset $DO_PARALLEL
>> >
>>
>> ?This should just be "unset DO_PARALLEL" (no $)
>> ?
>>
>>
>> > ./configure -cuda gnu
>> > make install
>> > make test (optional)
>> > make clean
>> > ./configure -cuda -mpi gnu (only needed if you want to run across 2 GPUs
>> > in a single job at the same time).
>> > make install
>> > export DO_PARALLEL='mpirun -np 2' (or whatever syntax your mpi uses)
>> > make test (optional)
>> > make clean
>> > unset $DO_PARALLEL
>> >
>>
>> T
>> ?his should also just be "unset DO_PARALLEL"
>>
>> I have nothing to add to the general advice here -- it is the typical
>> workflow for installing Amber in serial, parallel, and with CUDA. The wiki
>> page linked earlier goes into a little more detail, which will take longer
>> to work through but should hopefully provide more insight about what each
>> step is doing.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Tue, 30 Dec 2014 18:03:53 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] Need help in SMD
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3opfJ6TSVeG-AmeDj67TuJD=axqOZfnjJ4nwCqVb9JGzA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Tue, Dec 30, 2014 at 12:32 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com
>> > wrote:
>>
>> > Dear Users,
>> >
>> > I am using SMD for bond breaking process. Firstly I did minimization using
>> > DFTB and then heating and equlibration dynamics using QM/MM with DFTB.
>> > After that I went for bond stretching. During SMD calculation, it runs fine
>> > for 200 steps but stops suddenly without any error and it prints output for
>> > SMD.txt for 200 steps. I am unable to figure out the problem. I am using
>> > following input :
>> >
>> > Equlibration using QM potential
>> > &cntrl
>> > imin=0, nstlim=500000,
>> > dt=0.002, irest = 1, ntx = 7,
>> > ntt=3, pres0 = 1.0, ntp = 1,temp0=300.0,
>> > ntb=2,taup=2.0, ntr=1, restraint_wt=1000.0
>> >
>>
>> ?This restraint weight is WAYY too strong. Consider values at least 2 (if
>> not 3) orders of magnitude smaller than this. And if possible, don't use
>> positional restraints during your steered MD simulations.
>>
>> ntf=2, ntc=2,restraintmask=':5960,6503',
>> > cut=8.0, gamma_ln = 2.0,
>> > ifqnt=1,
>> > ntpr = 500, ntwr=500, ntwx = 500,
>> > /
>> > &qmmm
>> > qmmask=':13',
>> > qmcharge=-1,
>> > qm_theory='DFTB',
>> > qmcut=8.0,
>> > writepdb = 1
>> > /
>> >
>> > ncsu_smd
>> >
>> > output_file = 'smd.txt'
>> > output_freq = 500
>> >
>> > variable
>> > type = DISTANCE ! Distance
>> > i = (388,390)
>> > path = (X,5.0)
>> > harm = (50.0)
>> > end variable
>> >
>> > end ncsu_smd
>> >
>> > I want to vary the distance between atoms 388 and 390 by 5 angs, but it
>> > varies only for 1.47 to 1.49 angs. These atoms belong to residue 13 which
>> > is in QM region.
>>
>> I will be very much thankful if someone helps me to run it properly. Thanks
>> > in advance.
>> >
>>
>> ?I would also suggest looking at the output file for any hints about what
>> may have gone wrong. If you don't get any hints there, print out every
>> step to see if you can catch the problem happening that way. Problems with
>> SCF convergence may be due to large forces and strained calculations or a
>> bad choice for the QM region (there are certain bonds, that you should
>> never cut along the QM/MM boundary, like amide bonds, I think).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Tue, 30 Dec 2014 18:11:08 -0500
>> From: Jason Swails <jason.swails.gmail.com>
>> Subject: Re: [AMBER] WHAM tolerance
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAEk9e3qX_cxzdn=T7dZVW1FEivpVwi-JZ-_tMBXWd8Mzr66tog.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Thu, Dec 25, 2014 at 10:46 PM, Sun <sunbintyy.163.com> wrote:
>>
>> > Dear all,
>> >
>> > I studied the disassociation process of a ligand depart from an enzyme's
>> > active site by using the PMF method. The umbrella sampling and Weighted
>> > Histogram Analysis Method (WHAM) were used. However, when I used the WHAM
>> > to get final PMFs of this process, I found that the tolerance value, a
>> > parameter which specifies the convergence criteria of the WHAM calculation,
>> > influenced the free energy curve abnormally ( see the following figure).
>> >
>>
>> ?You didn't actually attach any figure.
>> ?
>>
>>
>> > In general sense, the smaller the tolerance, the more accurate the free
>> > energy will be. In my case, when tolerance was set to 0.1, the calculated
>> > binding free energy agreed with the experimental binding free energy quit
>> > well. However, when the tolerance became smaller, the deviation between
>> > calculated and experimental binding energy became larger, also the free
>> > energy curve became abnormal.
>> >
>> > So could anyone give me some advice about the possible factors that may
>> > cause this phenomenon ?
>> >
>>
>> ?Are you sure that you have sufficient overlap between the various
>> windows? That is, do the geometric distributions (e.g., distance, angle,
>> or torsions) along the PMF dimension for each window overlap with their
>> adjacent windows? If not, WHAM will not be able to "stitch" the various
>> windows back together and you will get nonsensical results.? You may need
>> to add more windows to ensure that you get good overlap. Not all methods
>> require windows to overlap (like the variational free energy profile
>> method), but WHAM does.
>>
>> See the end of the umbrella sampling tutorial, section 2, for a brief
>> discussion about this:
>> http://ambermd.org/tutorials/advanced/tutorial17/section2.htm
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> ------------------------------
>>
>> Message: 11
>> Date: Wed, 31 Dec 2014 17:27:14 +0530
>> From: Pallavi Mohanty <pallavipmohanty.gmail.com>
>> Subject: [AMBER] Need help in Targeted MD
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAN7+Y0+Zsao-L1pfCZwZ-CKZV36tfUGUTFH6EwcZenQsp4U9A.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Users,
>> I am running TMD in AMBER, at this point i am done with heating and
>> equilibration steps. I have an open and closed conformation and i want to
>> span the transition from open to closed.
>> My Input file for TMD was
>>
>> TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
>> &cntrl
>> imin = 0, ntx = 1, nstlim = 5000, irest = 0,
>> dt = 0.002, ntc = 2, ntf = 2, tol = 0.000001,
>> temp0 = 300.0,
>> cut = 10.0,
>> ntpr = 50, ntwx = 50, ntwr = 500,
>> ntb = 0, ntt = 1, tautp = 0.5, ntp = 0,
>> igb = 1, nscm = 0, nmropt = 1,
>> ntr = 1, restraint_wt = 0.02,
>> restraintmask = ":38-58,62-85,104-134",
>> itgtmd = 1, tgtrmsd = 1.6, tgtmdfrc = 1.0,
>> tgtrmsmask = "(:1-37,59-61,86-103)",
>> /
>> &wt
>> TYPE='TGTRMSD', istep1=1, istep2=1000,
>> value1 = 1.000, value2 = 0.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1=1000, istep2=0,
>> value1 = 0.0, value2 = 0.0,
>> /
>> &wt
>> type='END',
>> /
>> and I got an error stating "Targeted molecular dynamics:
>> tgtrmsd = 1.60000, tgtmdfrc= 1.00000
>> | INFO: Old style inpcrd file read "
>>
>> Please suggest where I have gone wrong.
>>
>> --
>> Regards,
>>
>> Pallavi Mohanty
>>
>>
>> ------------------------------
>>
>> Message: 12
>> Date: Wed, 31 Dec 2014 14:20:37 +0200
>> From: Kshatresh Dutta Dubey <kshatresh.gmail.com>
>> Subject: Re: [AMBER] Need help in SMD
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAF3NQ5cmVDg7emuZCGOguf9riMRsWVVikrZoQrcO0+_pMzBa3A.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi Jason,
>>
>> Thanks for your suggestions, I removed the restraint and everything went
>> fine.
>>
>> Regards
>> Kshatresh
>>
>> On Wed, Dec 31, 2014 at 1:03 AM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>>
>> > On Tue, Dec 30, 2014 at 12:32 PM, Kshatresh Dutta Dubey <
>> > kshatresh.gmail.com
>> > > wrote:
>> >
>> > > Dear Users,
>> > >
>> > > I am using SMD for bond breaking process. Firstly I did minimization
>> > using
>> > > DFTB and then heating and equlibration dynamics using QM/MM with DFTB.
>> > > After that I went for bond stretching. During SMD calculation, it runs
>> > fine
>> > > for 200 steps but stops suddenly without any error and it prints output
>> > for
>> > > SMD.txt for 200 steps. I am unable to figure out the problem. I am using
>> > > following input :
>> > >
>> > > Equlibration using QM potential
>> > > &cntrl
>> > > imin=0, nstlim=500000,
>> > > dt=0.002, irest = 1, ntx = 7,
>> > > ntt=3, pres0 = 1.0, ntp = 1,temp0=300.0,
>> > > ntb=2,taup=2.0, ntr=1, restraint_wt=1000.0
>> > >
>> >
>> > ?This restraint weight is WAYY too strong. Consider values at least 2 (if
>> > not 3) orders of magnitude smaller than this. And if possible, don't use
>> > positional restraints during your steered MD simulations.
>> >
>> > ntf=2, ntc=2,restraintmask=':5960,6503',
>> > > cut=8.0, gamma_ln = 2.0,
>> > > ifqnt=1,
>> > > ntpr = 500, ntwr=500, ntwx = 500,
>> > > /
>> > > &qmmm
>> > > qmmask=':13',
>> > > qmcharge=-1,
>> > > qm_theory='DFTB',
>> > > qmcut=8.0,
>> > > writepdb = 1
>> > > /
>> > >
>> > > ncsu_smd
>> > >
>> > > output_file = 'smd.txt'
>> > > output_freq = 500
>> > >
>> > > variable
>> > > type = DISTANCE ! Distance
>> > > i = (388,390)
>> > > path = (X,5.0)
>> > > harm = (50.0)
>> > > end variable
>> > >
>> > > end ncsu_smd
>> > >
>> > > I want to vary the distance between atoms 388 and 390 by 5 angs, but it
>> > > varies only for 1.47 to 1.49 angs. These atoms belong to residue 13 which
>> > > is in QM region.
>> >
>> > I will be very much thankful if someone helps me to run it properly. Thanks
>> > > in advance.
>> > >
>> >
>> > ?I would also suggest looking at the output file for any hints about what
>> > may have gone wrong. If you don't get any hints there, print out every
>> > step to see if you can catch the problem happening that way. Problems with
>> > SCF convergence may be due to large forces and strained calculations or a
>> > bad choice for the QM region (there are certain bonds, that you should
>> > never cut along the QM/MM boundary, like amide bonds, I think).
>> >
>> > HTH,
>> > Jason
>> >
>> > --
>> > Jason M. Swails
>> > BioMaPS,
>> > Rutgers University
>> > Postdoctoral Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> With best regards
>> ************************************************************************************************
>> Kshatresh Dutta Dubey
>> Post Doctoral Researcher,
>> Lise Meitner Center for Computational Quantum Chemistry
>> Hebrew University of Jerusalem Israel
>> Jerusalem, Israel
>>
>>
>> ------------------------------
>>
>> Message: 13
>> Date: Wed, 31 Dec 2014 09:35:08 -0500
>> From: David A Case <case.biomaps.rutgers.edu>
>> Subject: Re: [AMBER] Need help in Targeted MD
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20141231143508.GB58124.biomaps.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Wed, Dec 31, 2014, Pallavi Mohanty wrote:
>>
>> > I am running TMD in AMBER, at this point i am done with heating and
>> > equilibration steps. I have an open and closed conformation and i want to
>> > span the transition from open to closed.
>> > My Input file for TMD was
>> >
>> > TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
>> > &cntrl
>> > imin = 0, ntx = 1, nstlim = 5000, irest = 0,
>>
>> You are using irest=0, which would not be advised if you have already done
>> heating and equilibration. But this is unlikely to be the cause of your
>> problem.
>>
>> > and I got an error stating "Targeted molecular dynamics:
>> > tgtrmsd = 1.60000, tgtmdfrc= 1.00000
>> > | INFO: Old style inpcrd file read "
>>
>> This is not an error message. Set ntpr=1 and see if you get any useful
>> information from early steps. Make sure that all energies (except the
>> targetted stuff, which I assume you are now turning on for the first time)
>> are the same in the first step of the new run compared to the final step
>> of the equilibration.
>>
>> ...hope this helps....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 14
>> Date: Wed, 31 Dec 2014 09:55:15 -0500
>> From: Carlos Simmerling <carlos.simmerling.gmail.com>
>> Subject: Re: [AMBER] Need help in Targeted MD
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGk3s-TVgWNhcN7+Z23R+7ovTsuJc6caF4qqxqC3XX1Cw7E67g.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> I would also try running this on a single CPU, and carefully checking the
>> initial rmsd to the refcrd. It's not difficult to make mistakes in setting
>> masks, etc.
>> On Dec 31, 2014 9:35 AM, "David A Case" <case.biomaps.rutgers.edu> wrote:
>>
>> > On Wed, Dec 31, 2014, Pallavi Mohanty wrote:
>> >
>> > > I am running TMD in AMBER, at this point i am done with heating and
>> > > equilibration steps. I have an open and closed conformation and i want to
>> > > span the transition from open to closed.
>> > > My Input file for TMD was
>> > >
>> > > TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
>> > > &cntrl
>> > > imin = 0, ntx = 1, nstlim = 5000, irest = 0,
>> >
>> > You are using irest=0, which would not be advised if you have already done
>> > heating and equilibration. But this is unlikely to be the cause of your
>> > problem.
>> >
>> > > and I got an error stating "Targeted molecular dynamics:
>> > > tgtrmsd = 1.60000, tgtmdfrc= 1.00000
>> > > | INFO: Old style inpcrd file read "
>> >
>> > This is not an error message. Set ntpr=1 and see if you get any useful
>> > information from early steps. Make sure that all energies (except the
>> > targetted stuff, which I assume you are now turning on for the first time)
>> > are the same in the first step of the new run compared to the final step
>> > of the equilibration.
>> >
>> > ...hope this helps....dac
>> >
>> >
>> > _______________________________________________
>> > 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 1085, Issue 1
>> **************************************
>
>
>
> _______________________________________________
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 02 2015 - 10:30:04 PST
