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

Berk Hess gmx3 at hotmail.com
Thu Jan 31 15:56:01 CET 2008

> Date: Thu, 31 Jan 2008 15:29:50 +0100
> From: michael.bon at cea.fr
> To: gmx-users at gromacs.org
> Subject: RE : FEP : separating components of dgdl
> Hi,
> You were right for the bonds, I forgot that I was using constraints = all-bonds.
> Could the missing term be the soft core then ? Or is it included in VdW ?
No, those terms are always included.

> Anyway, I noticed that this problem of hidden extra term happens when I modify something else than a hydrogen. Does it make sense ?
> For example, I did N->DUM with all the parameters kept the same : every components of dVdl are 0 (VdW, Coulomb, angle, proper dihedral, Ryck.,  LJ 1-4, position restraint, disp. corr. ), but dVdl/dlambda is -6. Any idea ?

I have no clue.
But the easy way to find out is to take your system with only N->DUM
and do two runs of zero steps at two different lambda values and see which energy term
in the log file has changed.

> Other question : is there some information available about the "best" settings of soft core parameters with amber99 ?

As long as you are working with bio-molecules, the optimal soft-core parameters
are the same for all force-fields.


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

More information about the gromacs.org_gmx-users mailing list