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
unrelated.
One more Q', I saw your great gromacs tutor...@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.
-Justin
Best,
Juju
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@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.
-Justin
> 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
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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