[gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 121

sunita at tifrh.res.in sunita at tifrh.res.in
Thu Jan 28 14:00:25 CET 2016


Dear users,

I got one reference where water properties at high temperature was
studied. However, was done with amber force field. The RDF analysis at
different temperatures would provide answer to my query which were done
using GROMOS96 54a7 force field.

Properties of pure water and sodium chloride solutions at high
temperatures and pressures:a simulation study
http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.992019?journalCode=gmos20

Thanks.
Sunita


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> Today's Topics:
>
>    1. Re: Simulation runs indefinitely (Justin Lemkul)
>    2. Re: High temperature simulation with GROMOS96 54a7 (Justin Lemkul)
>    3. Re: Simulation runs indefinitely (Mark Abraham)
>    4. Re: Simulation runs indefinitely (anu chandra)
>    5. Define custom moltype for free energy calculations (Tom Newport)
>    6. Re: Simulation runs indefinitely (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Jan 2016 07:45:33 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simulation runs indefinitely
> Message-ID: <56A8BBED.2000607 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 1/27/16 6:28 AM, anu chandra wrote:
>> Hello Gromcas users,
>>
>> I having been simulating few membrane-protein systems for about ~300ns,
>> using a 20 ns window for each run. Though I used the command ' gmx_mpi
>> convert-tpr -s md20.tpr -f md20.cpt -e md20.edr -o md21.tpr -extend
>> 20000 '
>> to generate the tpr file for the next run, interestingly, one of the
>> system
>> ran for ~26000 ps and only got terminates once the run reached
>> wall-clock
>> time. All other systems terminates after successfully completing 20000
>> ps,
>> as prescribed.  I just wonder why simulation of one of the system
>> continued
>> indefinitely, as rest of the systems behaved as expected. All systems
>> have
>> almost same composition, just differ in the ion concentration.
>>
>
> There must be some problem in your script when you're creating the input.
> mdrun
> doesn't decide to run any number of steps it likes.  Probably you've
> failed to
> supply a checkpoint file, so the run starts over from the beginning in
> that
> instance.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 Jan 2016 07:46:16 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] High temperature simulation with GROMOS96
> 	54a7
> Message-ID: <56A8BC18.2060607 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 1/27/16 7:20 AM, sunita at tifrh.res.in wrote:
>> Dear gmx-users,
>>
>> I have a short question. Did GROMACS recent force field "GROMOS96 54a7
>> force field" parametrize for high temperature classical MD simulation
>> such
>> as 353 K?
>>
>> Is there any reference paper?
>>
>
> The reference is given in the manual.  Start there.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 27 Jan 2016 12:47:08 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Simulation runs indefinitely
> Message-ID:
> 	<CAMNuMASFiq0YZVOFqv-FyprHFPj8+JFLfFtxiWRV2T5W2QJL5Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> As suggestion suggests, you probably didn't do what you think you did,
> particularly with restarting from the checkpoint. Do a diff on your log
> files to see what was different.
>
> Mark
>
> On Wed, Jan 27, 2016 at 1:46 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/27/16 6:28 AM, anu chandra wrote:
>> > Hello Gromcas users,
>> >
>> > I having been simulating few membrane-protein systems for about
>> ~300ns,
>> > using a 20 ns window for each run. Though I used the command ' gmx_mpi
>> > convert-tpr -s md20.tpr -f md20.cpt -e md20.edr -o md21.tpr -extend
>> 20000 '
>> > to generate the tpr file for the next run, interestingly, one of the
>> system
>> > ran for ~26000 ps and only got terminates once the run reached
>> wall-clock
>> > time. All other systems terminates after successfully completing 20000
>> ps,
>> > as prescribed.  I just wonder why simulation of one of the system
>> continued
>> > indefinitely, as rest of the systems behaved as expected. All systems
>> have
>> > almost same composition, just differ in the ion concentration.
>> >
>>
>> There must be some problem in your script when you're creating the
>> input.
>> mdrun
>> doesn't decide to run any number of steps it likes.  Probably you've
>> failed to
>> supply a checkpoint file, so the run starts over from the beginning in
>> that
>> instance.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 27 Jan 2016 13:35:39 +0000
> From: anu chandra <anu80125 at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Simulation runs indefinitely
> Message-ID:
> 	<CADEHHN=33Z+vg_N1FkOf+XF9Ym4ru47+-2zNwq=wVjw9X0htNg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Many thanks for the reply. I just created tpr file once again to see the
> output message. But, it looks like convert-tpr showing something different
> from it suppose to write about the steps. The only difference in the
> previous run was that it carried out with single GPU node.
>
> *******************************************************************************************************
> GROMACS:      gmx convert-tpr, VERSION 5.0.5
> Executable:   /usr/local/Cluster-Apps/gromacs/impi/5.0.5/bin/gmx_mpi
> Library dir:  /usr/local/Cluster-Apps/gromacs/impi/5.0.5/share/gromacs/top
> Command line:
>   gmx_mpi convert-tpr -s 18md.tpr -f 18md.cpt -e 18md.edr -o 19md.tpr
> -extend 20000
>
> Reading toplogy and stuff from 18md.tpr
> Reading file 18md.tpr, VERSION 5.0.5 (single precision)
>
> NOTE: Reading the state from trajectory is an obsolete feature of gmx
> convert-tpr.
>       Continuation should be done by loading a checkpoint file with mdrun
> -cpi
>       This guarantees that all state variables are transferred.
>       gmx convert-tpr is now only useful for increasing nsteps,
>       but even that can often be avoided by using mdrun -maxh
>
> NOTE: The simulation uses pressure coupling and/or stochastic dynamics.
> gmx convert-tpr can not provide binary identical continuation.
> If you want that, supply a checkpoint file to mdrun
>
>
> READING STATE FROM CHECKPOINT 18md.cpt...
>
> Extending remaining runtime of by 20000 ps (now 17529120 steps)
> Writing statusfile with starting step  138970880 and length   17529120
> steps...
>                                  time 277941.760 and length  *35058.240
> ps*
>
> gcq#333: "History has expired" (PubMed Central)
> ***************************************************************************************************
>
> It written *35058.240 ps *instead of *20000ps. *I usually use mdrun as '
> -cpi 18md.cpt -deffnm 19md '
>
>
> Many thanks
> Anu
>
> On Wed, Jan 27, 2016 at 12:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> As suggestion suggests, you probably didn't do what you think you did,
>> particularly with restarting from the checkpoint. Do a diff on your log
>> files to see what was different.
>>
>> Mark
>>
>> On Wed, Jan 27, 2016 at 1:46 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>> >
>> >
>> > On 1/27/16 6:28 AM, anu chandra wrote:
>> > > Hello Gromcas users,
>> > >
>> > > I having been simulating few membrane-protein systems for about
>> ~300ns,
>> > > using a 20 ns window for each run. Though I used the command '
>> gmx_mpi
>> > > convert-tpr -s md20.tpr -f md20.cpt -e md20.edr -o md21.tpr -extend
>> > 20000 '
>> > > to generate the tpr file for the next run, interestingly, one of the
>> > system
>> > > ran for ~26000 ps and only got terminates once the run reached
>> wall-clock
>> > > time. All other systems terminates after successfully completing
>> 20000
>> > ps,
>> > > as prescribed.  I just wonder why simulation of one of the system
>> > continued
>> > > indefinitely, as rest of the systems behaved as expected. All
>> systems
>> > have
>> > > almost same composition, just differ in the ion concentration.
>> > >
>> >
>> > There must be some problem in your script when you're creating the
>> input.
>> > mdrun
>> > doesn't decide to run any number of steps it likes.  Probably you've
>> > failed to
>> > supply a checkpoint file, so the run starts over from the beginning in
>> that
>> > instance.
>> >
>> > -Justin
>> >
>> > --
>> > ==================================================
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> >
>> > Department of Pharmaceutical Sciences
>> > School of Pharmacy
>> > Health Sciences Facility II, Room 629
>> > University of Maryland, Baltimore
>> > 20 Penn St.
>> > Baltimore, MD 21201
>> >
>> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> > http://mackerell.umaryland.edu/~jalemkul
>> >
>> > ==================================================
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 27 Jan 2016 14:50:29 +0000
> From: Tom Newport <tom.newport at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Define custom moltype for free energy
> 	calculations
> Message-ID:
> 	<CABRO9U3ZdJ6OPNr1Nj4RsjP1UsMXLd-zfZb2jZhLppWxD6U4vQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> To give some background, I would like to be able to perform free energy
> calculations using a variety of different fairly complex selections to
> specify which bits of the system to turn on or off. These may include
> several proteins and several different ligands. There are other proteins
> and ligands which I do not want to include. This is for coarse-grained
> (martini) simulation of proteins and lipids, although I assume that
> doesn't
> make a difference.
>
> So, how is a moltype specified in GROMACS, and what is the least messy way
> of adding several molecules to one moltype? (or can this be specified more
> easily, say through using an index file?)
>
> Any help greatly appreciated!
>
> Tom
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 27 Jan 2016 16:12:39 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Simulation runs indefinitely
> Message-ID:
> 	<CAMNuMASgAVLg7bv=5oFjn_z9Kxjv+8wj6AdmzhS4NeaQ8VCh2Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> You extended the run time of the tpr file, but mdrun only knows it has a
> tpr that asks for a number of steps, and that the input checkpoint file
> starts at whatever step it does. If you give it a checkpoint that is from
> much earlier in the run, then there's no way for it to know you intended
> something else.
>
> Mark
>
> On Wed, 27 Jan 2016 14:36 anu chandra <anu80125 at gmail.com> wrote:
>
>> Many thanks for the reply. I just created tpr file once again to see the
>> output message. But, it looks like convert-tpr showing something
>> different
>> from it suppose to write about the steps. The only difference in the
>> previous run was that it carried out with single GPU node.
>>
>>
>> *******************************************************************************************************
>> GROMACS:      gmx convert-tpr, VERSION 5.0.5
>> Executable:   /usr/local/Cluster-Apps/gromacs/impi/5.0.5/bin/gmx_mpi
>> Library dir:
>> /usr/local/Cluster-Apps/gromacs/impi/5.0.5/share/gromacs/top
>> Command line:
>>   gmx_mpi convert-tpr -s 18md.tpr -f 18md.cpt -e 18md.edr -o 19md.tpr
>> -extend 20000
>>
>> Reading toplogy and stuff from 18md.tpr
>> Reading file 18md.tpr, VERSION 5.0.5 (single precision)
>>
>> NOTE: Reading the state from trajectory is an obsolete feature of gmx
>> convert-tpr.
>>       Continuation should be done by loading a checkpoint file with
>> mdrun
>> -cpi
>>       This guarantees that all state variables are transferred.
>>       gmx convert-tpr is now only useful for increasing nsteps,
>>       but even that can often be avoided by using mdrun -maxh
>>
>> NOTE: The simulation uses pressure coupling and/or stochastic dynamics.
>> gmx convert-tpr can not provide binary identical continuation.
>> If you want that, supply a checkpoint file to mdrun
>>
>>
>> READING STATE FROM CHECKPOINT 18md.cpt...
>>
>> Extending remaining runtime of by 20000 ps (now 17529120 steps)
>> Writing statusfile with starting step  138970880 and length   17529120
>> steps...
>>                                  time 277941.760 and length  *35058.240
>> ps*
>>
>> gcq#333: "History has expired" (PubMed Central)
>>
>> ***************************************************************************************************
>>
>> It written *35058.240 ps *instead of *20000ps. *I usually use mdrun as '
>> -cpi 18md.cpt -deffnm 19md '
>>
>>
>> Many thanks
>> Anu
>>
>> On Wed, Jan 27, 2016 at 12:47 PM, Mark Abraham
>> <mark.j.abraham at gmail.com>
>> wrote:
>>
>> > As suggestion suggests, you probably didn't do what you think you did,
>> > particularly with restarting from the checkpoint. Do a diff on your
>> log
>> > files to see what was different.
>> >
>> > Mark
>> >
>> > On Wed, Jan 27, 2016 at 1:46 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>> >
>> > >
>> > >
>> > > On 1/27/16 6:28 AM, anu chandra wrote:
>> > > > Hello Gromcas users,
>> > > >
>> > > > I having been simulating few membrane-protein systems for about
>> ~300ns,
>> > > > using a 20 ns window for each run. Though I used the command '
>> gmx_mpi
>> > > > convert-tpr -s md20.tpr -f md20.cpt -e md20.edr -o md21.tpr
>> -extend
>> > > 20000 '
>> > > > to generate the tpr file for the next run, interestingly, one of
>> the
>> > > system
>> > > > ran for ~26000 ps and only got terminates once the run reached
>> > wall-clock
>> > > > time. All other systems terminates after successfully completing
>> 20000
>> > > ps,
>> > > > as prescribed.  I just wonder why simulation of one of the system
>> > > continued
>> > > > indefinitely, as rest of the systems behaved as expected. All
>> systems
>> > > have
>> > > > almost same composition, just differ in the ion concentration.
>> > > >
>> > >
>> > > There must be some problem in your script when you're creating the
>> input.
>> > > mdrun
>> > > doesn't decide to run any number of steps it likes.  Probably you've
>> > > failed to
>> > > supply a checkpoint file, so the run starts over from the beginning
>> in
>> > that
>> > > instance.
>> > >
>> > > -Justin
>> > >
>> > > --
>> > > ==================================================
>> > >
>> > > Justin A. Lemkul, Ph.D.
>> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> > >
>> > > Department of Pharmaceutical Sciences
>> > > School of Pharmacy
>> > > Health Sciences Facility II, Room 629
>> > > University of Maryland, Baltimore
>> > > 20 Penn St.
>> > > Baltimore, MD 21201
>> > >
>> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> > > http://mackerell.umaryland.edu/~jalemkul
>> > >
>> > > ==================================================
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or
>> > > send a mail to gmx-users-request at gromacs.org.
>> > >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 141, Issue 121
> *******************************************************
>




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