[gmx-users] Pressure from Ke and Virial from .edr

[Justin Lemkul]

On 8/13/15 10:21 AM, Hardy, Adam wrote:
> Dear All,
>
> As part of my work I need to recalculate the pressure from the kinetic energy and virial.
>
> I start with the equation (2/V)(Ke – Vir).
>
> The units given for the virial and kinetic energy (as taken from the .edr file) are given in kJ/mol so when I calculate the values of the pressure components and convert units I’m left with a pressure in Bar/mol (kJ/m^3 mol -> 10^3 Pa/mol -> 10^-2 Bar/mol). My initial thought was to multiply by Avogadro’s number but this gives me a number that is~750 times too large so clearly I’m missing something. Where am I going wrong?
>

See calc_pres() in src/gromacs/mdlib/coupling.c

-Justin

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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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