[gmx-users] Pressure estimation from NVT
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 27 00:21:10 CEST 2011
Dallas Warren wrote:
> Have you looked at the data from which you calculated the pressure
> average from?
Very important point. There was a bug in pressure-related output in Gromacs
versions up to, and including 4.5.3. The instantaneous values are correct, but
the averages are flawed.
> Catch ya,
> Dr. Dallas Warren
> Medicinal Chemistry and Drug Action
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
> +61 3 9903 9304
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
> *From:* gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Sikandar Mashayak
> *Sent:* Tuesday, 27 September 2011 3:48 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Pressure estimation from NVT
> I am trying to determine pressure of water at given density and
> temperature using SPC/E water model. To achieve this, I am doing NVT
> bulk simulations and then using g_energy I get average pressure values.
> The question I have is how accurate these average pressure predictions are?
> e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water
> density, but theoretical value for it is around 1 bar. What are the
> possible reasons for this much deviation from theoretical value? Is
> there anything wrong with my set up? I am using 2141 water molecules in
> 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD
> algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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