[gmx-users] Pressure estimation from NVT

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 27 17:09:11 CEST 2011

Sikandar Mashayak wrote:
> Hi
> @ 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 

Not "may be" - they are.  There was a bug:


> pressure explicitly from instantaneous P values in trajectory?

Upgrade to version 4.5.4 - there's nothing wrong with the values stored in the 
.edr file, just the analysis of them.  It's more accurate to use the .edr file 
since it has a complete energy history.

> @ 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? 

Pressure is an incredibly fickle quantity.  See the extensive discussions in the 
list archive about the ability to obtain proper values and their statistical 
interpretation.  It's been discussed countless times, even very recently.


> thanks
> sikandar
> On Mon, Sep 26, 2011 at 8:51 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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