Re: [gmx-users] topology treatment in free energy calculations -possible bug

2008-01-07 Thread Maik Goette
e A-state parameters are also determined by the atom type. Berk. From: Maik Goette <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GMX-mailinglist Subject: [gmx-users] topology treatment in free energy calculations -possible bug Date: Fri, 04 Jan 2008 15:15:57 +0100 Hi

Re: [gmx-users] topology treatment in free energy calculations - possible bug

2008-01-04 Thread bharat v. adkar
On Fri, 4 Jan 2008, Maik Goette wrote: Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by G

RE: [gmx-users] topology treatment in free energy calculations -possible bug

2008-01-04 Thread Berk Hess
the B-parameters to be looked up based on atom-type. You would only want that when the A-state parameters are also determined by the atom type. Berk. From: Maik Goette <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GMX-mailinglist Subject: [gmx-users] topology treatment in

Re: [gmx-users] topology treatment in free energy calculations - possible bug

2008-01-04 Thread David Mobley
Maik > I just found a strange behaviour of GROMACS, when processing topologies > with B-values. Maybe I just think of it as unintuitive/bug, but here we go: > > e.g. OPLS > > Consider an angle given (all atoms have B-values, which angle-parameter > can be found by GROMACS in the bonded.itp for the

[gmx-users] topology treatment in free energy calculations - possible bug

2008-01-04 Thread Maik Goette
Hi I just found a strange behaviour of GROMACS, when processing topologies with B-values. Maybe I just think of it as unintuitive/bug, but here we go: e.g. OPLS Consider an angle given (all atoms have B-values, which angle-parameter can be found by GROMACS in the bonded.itp for the A- and B-