[gmx-users] Free energy of dihedral restraint

David Mobley dmobley at gmail.com
Sat Mar 22 01:51:12 CET 2008


I don't believe that it is implemented. Developers: It probably should
be, since the other restraints can be perturbed.

In the interim, it's pretty straightforward to compute the dV/dlambda
for restraining from the restraint energy if you know the value of the
dihedral angle (which you can easily compute). Of course this requires
some postprocessing.


On Mon, Mar 17, 2008 at 10:01 AM, Robert Johnson
<bobjohnson1981 at gmail.com> wrote:
> Hello everyone,
>  I posted this question a week ago and no one commented on it. I would
>  appreciate it if someone could answer this. I would like to compute
>  the free energy of turning on orientation restraints (1 distance, 2
>  angle, 3 dihedral). I'm using Gromacs v. 3.3.1 and there doesn't seem
>  to be a way to perturb the dihedral restraints section of the topology
>  file. Has this feature been implemented in v. 3.3.3? I didn't see any
>  documentation about this in the revision history. Are there plans to
>  implement this at some point? It is possible to perturb distance and
>  angle restraints, but it looks like dihedral restraints are treated
>  differently. For example, grompp doesn't even list dihedral restraints
>  when outputting the total number of bonded interactions.
>  Thanks,
>  Bob
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