[gmx-users] where are Density and Volume?

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 13 20:28:10 CEST 2011 


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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>  >  > 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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> 

-- 
========================================

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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