[gmx-users] Check V for NVT
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 14 00:44:45 CEST 2010
Rama G wrote:
> Thanks Justin,
> but I did not find them, what I found are Vir-XY, YZ, XX,....
> Are these the same as Box-X, Y, Z, or perhaps can be converted to?
> Btw, I am using 4.0.7 version.
See the latest post in the thread. The Vir-* terms refer to virial, which is
> One more Q', I saw your great gromacs tutorial at VT, but I am kinda
> confused you used both NPT and NVT in position restraint step,
> while 'official' tutorial by JE Kerrigan only used NPT, would that
> affect the final results? Sorry, newbie here.
Are any of the tutorials "official"? They're all just contributed by users...
In any case, the "typical" equilibration steps involve both NVT (to relax
temperature), then NPT (to relax pressure once temperature is stable). In some
cases, if you apply NPT directly, bad clashes in the initial structure can cause
temperature spikes, thus kinetic energy spikes, the virial (and thus pressure)
goes haywire, and the whole system collapses. Not always the case, but I've
noticed that this can happen. Maybe there's a more deeply theoretical reason
for NVT prior to NPT, but I've never found one aside from stability issues.
Some systems are robust enough to proceed to NPT immediately, but most often in
the literature NVT precedes NPT.
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Fri, August 13, 2010 3:23:40 PM
> *Subject:* Re: [gmx-users] Check V for NVT
> Rama G wrote:
> > Hi Gmx users,
> > I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I
> wanna check if the Volume is constant after the simulation.
> > I tried g_energy but did not find "Volume" in the pool of the
> options. Can anyone help me?
> Box-X, -Y, and -Z are in the .edr file. From these, you can calculate
> the volume.
> > Thanks,
> > Juju
> -- ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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