[gmx-users] want to calculate pressure from virial

David van der Spoel spoel at xray.bmc.uu.se
Wed May 13 07:05:13 CEST 2009

anirban polley wrote:
> Dear Sir,
>            I want to calculate virial, hence pressure.
> PV=NKT-1/3 * < sum of (r * f)>
>           where r is displacement and f is internal force.  Now, how can 
> I proceed?
> 1. g_traj -f name.trr -af gives me force and each velocity with time?
> Now, question, is the force given in data is only due to internal force 
> or total force on each atom?
> Am I right if I use this force and position of the atom to calculate virial.
> 2. If I am wrong, then please tell me how I can calculate Virial, and 
> hence pressure.
> 3. I saw that g_energy -f name.edr -vis gives pressure, virial and all 
> the stuffs. I want to know that how I can calculate it myself.
The manual describes how gromacs does it.

> 4. Can you tell me how I can calculate pressure change with z - axis 
> where I am simulating Bilayer Membrane.
> Thanking You,
> Anirban
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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