[gmx-users] where are Density and Volume?
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 13 23:22:26 CEST 2011
Yao Yao wrote:
> Hi Justin,
>
> Just curious. what is inside .cpt file,is there a way I can change it in
> readable format?
gmxdump
> I also notice that every mdrun step I got a state.cpt and state_prev.cpt
> as well, any difference between the two?
http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
> And using .cpt seems a little faster (a couple of hours or so) than
> without using it for the same time length simulation, do you happen to
> know the reason?
When supplying the .cpt to grompp, or to mdrun? If you supply it to mdrun, the
simulation picks up from the time in the .cpt file, not the .tpr file.
At this point, you should probably start a new thread about checkpoints, rather
than add on to this one, as the issues are now unrelated.
-Justin
>
> Thanks,
>
> yao
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Thursday, October 13, 2011 11:28 AM
> *Subject:* Re: [gmx-users] where are Density and Volume?
>
>
>
> Yao Yao wrote:
> > Hi, Justin
> >
> > Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to
> mdrun/continue NVE production run.
> > So though I did not set V or P constraint in NVE mdp, it still keeps
> them as constant, like my NVE did not work.
> > Am I supposed to do so if I wanna simulate NVE?
> >
>
> NVE will keep the energy constant under the set conditions. I do not
> know why P is constant; with V being constant (by definition), P should
> fluctuate under NVE. Providing a .cpt file from a previous NVT or NPT
> will define the conditions under which NVE is run (i.e. what energy is
> to be maintained).
>
> -Justin
>
> > Thanks,
> >
> > Yao
> >
> > ------------------------------------------------------------------------
> > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> > *Sent:* Thursday, October 13, 2011 10:42 AM
> > *Subject:* Re: [gmx-users] where are Density and Volume?
> >
> >
> >
> > Yao Yao wrote:
> > > Hi Justin,
> > >
> > > thanks,
> > >
> > > that is just initial value, no fluctuation over time.
> > >
> >
> > Right. The volume is constant, therefore the initial values of
> density and volume are always the same.
> >
> > -Justin
> >
> > > yao >
> ------------------------------------------------------------------------
> > > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
> > > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
> > > *Sent:* Thursday, October 13, 2011 10:24 AM
> > > *Subject:* Re: [gmx-users] where are Density and Volume?
> > >
> > >
> > >
> > > Yao Yao wrote:
> > > > Hi Justin,
> > > >
> > > > It is NVE. Is there a consistent way I can know my D and V?
> > > >
> > >
> > > Then you've got the same case as NVT (for these values, anyway) -
> volume and density are fixed at whatever value they started at.
> editconf should have printed this somewhere along the way.
> > >
> > > -Justin
> > >
> > > > Thanks,
> > > >
> > > > Yao
> > > >
> > > >
> ------------------------------------------------------------------------
> > > > *From:* Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
> > > > *To:* Yao Yao <yao0o at ymail.com <mailto:yao0o at ymail.com>
> <mailto:yao0o at ymail.com <mailto:yao0o at ymail.com>>
> <mailto:yao0o at ymail.com <mailto:yao0o at ymail.com> <mailto:yao0o at ymail.com
> <mailto:yao0o at ymail.com>>>>; Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
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> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>>
> > > > *Sent:* Thursday, October 13, 2011 9:58 AM
> > > > *Subject:* Re: [gmx-users] where are Density and Volume?
> > > >
> > > >
> > > >
> > > > Yao Yao wrote:
> > > > > Hi,
> > > > >
> > > > > I wanna get Density and Volume of my system after simulation.
> > > > > I found in tutorials by Justin and kerrigan?, that g_energy
> -f *.edr -o should work,
> > > > > but I do not find in my version 4.5.1 and 4.5.4. That is
> kind of weird.
> > > > >
> > > >
> > > > Was it an NVT simulation? If so, those terms are not written
> because they are, by definition, constant.
> > > >
> > > > -Justin
> > > >
> > > > -- ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Ph.D. Candidate
> > > > ICTAS Doctoral Scholar
> > > > MILES-IGERT Trainee
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
> > > >
> > > >
> > >
> > > -- ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
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> > > > ========================================
> > > >
> > > >
> > >
> > > -- ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
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> > -- ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
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> > > > jalemkul[at]vt.edu | (540) 231-9080
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> > > >
> > > > ========================================
> > > >
> > > >
> > >
> > > -- ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
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> > > >
> > > > ========================================
> > > >
> > > >
> > >
> > > -- ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
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> > -- ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
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>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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