Re: [gmx-users] where are Density and Volume?

[Justin A. Lemkul]

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 <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 <mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org 
<mailto: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> 
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
 >  > *To:* Yao Yao <ya...@ymail.com <mailto:ya...@ymail.com> 
<mailto:ya...@ymail.com <mailto:ya...@ymail.com>>>; Discussion list for 
GROMACS users <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> 
<mailto: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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 >  > ========================================
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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@gromacs.org 
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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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--
========================================

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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