[gmx-users] Scalar virial

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 5 09:52:55 CET 2006

Tandia, Adama wrote:
> Dear All,
> I'm running a NVT MD where I quench a system from 3000K to 1000K. At the
> end of the quench,  I want to use the following relation:
> 	P = Rho*k_B*T + (1/3V) * < Sum_{i<j}[F(r_ij).r_ij] >
> where Rho is a number density, V the volume of the system, and k_B the
> Boltzmann constant.
> 1- How can one extract the scalar virial (< Sum_{i<j}[F(r_ij).r_ij] >)
> from the simulation?
> 2- I have considered taking the scalar virial as
> (1/3)(virial_XX+virial_YY+virial_ZZ) from the virial tensor, and
> recalculate the pressure but there seems to be a problem in the values.
> The pressure that I have from this calculation is very different from
> that one calculated from the trace of the pressure tensor. I saw on the
> list there was a bug in the virial calculation. Has this been fixed in
> the version 3.2.1?
> Anyone has an idea what is going on?
> I thank you all very much in advance for your prompt answer.
Try to compute the scalar virial from the pressure and the kinetic 
energy, using:

P = (2/V) [ Ekin - Vir ] (chapter 3.4)

And see how it compares. Note that you need a conversion factor from MD 
units to bar for the pressure. The factor is roughly 16.6

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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