[gmx-users] where are Density and Volume?

Yao Yao yao0o at ymail.com
Thu Oct 13 20:21:19 CEST 2011


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 <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>
> *To:* Discussion list for GROMACS users <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>>
>  > *To:* Yao Yao <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>>
>  > *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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> 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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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>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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
> 
> ========================================
> -- 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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