[gmx-users] where are Density and Volume?
Yao Yao
yao0o at ymail.com
Thu Oct 13 23:16:38 CEST 2011
Hi Justin,
Just curious. what is inside .cpt file,is there a way I can change it in readable format?
I also notice that every mdrun step I got a state.cpt and state_prev.cpt as well, any difference between the two?
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?
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>
> *To:* Discussion list for GROMACS users <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>>
> > *To:* Discussion list for GROMACS users <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>>>
> > > *To:* Yao Yao <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>>>
> > > *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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> > > ========================================
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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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> 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
> >
> > ========================================
> > -- gmx-users mailing list 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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> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
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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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