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?
Thanks,
Yao
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> > *To:* Yao Yao <ya...@ymail.com <mailto:ya...@ymail.com>>; Discussion list
>for GROMACS users <gmx-users@gromacs.org <mailto:gmx-users@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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> > 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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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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> 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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