[gmx-users] pressure dependence on volume.

[Justin Lemkul]

On 10/17/14 11:49 AM, Johnny Lu wrote:
> At least for real water, a 0.2% error in volume can mean the pressure is
> ~30 bar when the target pressure is 1 bar.
> http://docs.engineeringtoolbox.com/documents/309/water-density-temperature-pressure_2.png
>
> On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
>> Hi.
>>
>> Mainly TIP3P water, 300K. The pressure is near 1 bar.
>>
>> A less than 1% error in volume would cause how much error in average
>> pressure?
>>
>>  From three npt simulations of 72 ns with Berendsen barostat, I get the
>> average volume is 298.5 nm^3.
>>
>> Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
>> deviation from this volume), I run NVT simulation that at first gives a
>> system that doesn't seem to be at equilibrium.
>>

Does that time point correspond to the desired pressure?  The pressure tensor is 
calculated from the virial and the kinetic energy, so those are the quantities 
you should be looking at for instantaneous pressures.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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