[gmx-users] topology treatment in free energy calculations - possible bug
bharat v. adkar
bharat at sscu.iisc.ernet.in
Fri Jan 4 17:07:12 CET 2008
On Fri, 4 Jan 2008, Maik Goette wrote:
> 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-state):
> Original topology entry:
> 10 12 14 1
> Manually edited entry (with the correct ff-term):
> 10 12 14 1 109.700 669.440
> Now, a dump from the tpr-files yields the following:
> functype=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09500e+02,
> ctB= 2.92880e+02
> functype=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02,
> ctB= 6.69440e+02
> Now, what obviously happens is, that GROMACS searches the entries of the
> angle in the FF for both states and uses them in the case of the original
> If one puts a manual entry into the topology for the A-state though, the
> B-state is simply copied, instead of searched by GROMACS.
> This, IMHO, is quite inconvenient. Is this a bug or a feature?
it cannot be called as a bug... when you mention parameters for A state
in topology explicitly then grompp will expect you to mention the B state
parameters also, and if it doesn't find it, it will assign A state
parameter to B state. that is quite well documented, i think, in manual.
So there is no reason to think it as a bug.
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