[gmx-users] RE: RE : FEP : separating components of dgdl

Berk Hess gmx3 at hotmail.com
Tue Jan 29 10:32:08 CET 2008

> Date: Tue, 29 Jan 2008 10:24:57 +0100
> From: michael.bon at cea.fr
> To: gmx-users at gromacs.org
> Subject: RE : FEP : separating components of dgdl
> Thanks for the quick reply.
> I have an other question : I ran a quick simulation on a single node using mdrun -sepdvdl and the components are written in
> the .log file. But the final value of dVpot/dlambda doesn't seem to be the sum of the components above. Example for some step:
> VdW and Coulomb SR : dVdl -2.72859e+02
> Angle :              dVdl  3.56537e+00
> Proper Dih. :        dVdl -7.31260e-03
> Ryckaert-Bell. :     dVdl -1.13654e-01
> LJ-14 + Coulomb-14 : dVdl  6.39499e+02
> Dispersion correc. : dVdl  0.00000e+00
> And I read : dVpot/dlambda = 3.62310e+02, instead of 3.70e+02.
> There is no PME in this sim.
> What did I forget ?

I assume you are running single processor.
The terms are per processor.

I think that the only contributions that are no added are:
constraints, only when you change constraint lengths,
kinetic energy, only when you change masses.

So do you change constraint lengths or masses?


Express yourself instantly with MSN Messenger! Download today it's FREE!

More information about the gromacs.org_gmx-users mailing list