[gmx-users] Pressure estimation from NVT

Sikandar Mashayak symashayak at gmail.com
Tue Sep 27 17:05:19 CEST 2011


@ Dallas and Justin

Do you mean that for gromacs version 4.5.3 averages computed using g_energy
may be flawed? And are you suggesting to compute average pressure explicitly
from instantaneous P values in trajectory?

@ Mark

Thanks for suggestion. I am doing 500 ps of equilibration and 10 ns of
production runs with 2141 molecules.

So the important point that I want to understand is that if I use the right
averaging or newer gromacs version, and do large system with longer
production runs, how accurate is the estimate of pressure values from bulk
water NVT simulations?


On Mon, Sep 26, 2011 at 8:51 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 27/09/2011 3:48 AM, Sikandar Mashayak wrote:
>> Hi
>> 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 electrostatics.
> The length of your simulation, and the absence of the equilibration period
> from your data collection are also critical factors in obtaining accurate
> converged averages, but usually neglected when people report what might be
> anomalies... please see http://www.gromacs.org/**
> Documentation/Terminology/**Pressure<http://www.gromacs.org/Documentation/Terminology/Pressure>
> Mark
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