From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Subject: [gmx-users] force field parameters/B state dihedrals
Date: Thu, 20 Jul 2006 15:07:35 -0700
Dear all,
I'm setting up some relative free energy calculations involving
changing atom types, and I have a related question about topologies.
In the dihedrals section, if my force field contains parameters for
the dihedral states organized by bond type, these are automatically
filled in when no parameters are specified in the topology.
On the other hand, if I specify parameters in the topology file for A
and B states, these are use instead of those specified for the force
field.
What happens if I specify parameters in the topology file for only the
A state? Does the B state:
(a) automatically use the parameters specified by the A state, or
(b) first check the force field for parameters, only using those
specified by the A state if it finds none?
I know that in cases where I specify parameters for only the A state,
and none are found in the force field, the B state uses the same A
state parameters. My question is what happens when B state parameters
could be specified by the force field, as this seems somewhat
ambiguous...
We have had a discussion about this some time ago
and we have changed the behavior for Gromacs 3.3.
In 3.3, when you give A state parameters only, they are
always copied to the B state. If you did not specify B state
parameters a warning is issued, as this is indeed somewhat ambiguous.
Unfortunately it seems that we forgot to describe this situation
in the manual.
So the B state parameters are only searched for using the B state
atom types when also no A state parameters have been supplied.
Note that there is still ambiguity when one specifies
A and B state parameters in the bonded types sections.
This issue has not been resolved yet.
Berk.
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