[gmx-users] Accessing the distance_restraints energy term
Mark.Abraham at anu.edu.au
Thu Nov 6 04:42:34 CET 2008
chris.neale at utoronto.ca wrote:
> I can't seem to get the energetic contribution from distance restraints
> in gmx 3.3.1, 3.3.3, or 4.0
> I am using Mark Abraham's incantation of the charmm ff in gromacs. Here,
> distance_restraints are used to deal with Charmm's Urey-Bradley
Not true. Yuguang Mu's version did so because at the time he wrote his,
the native U-B was not available in GROMACS. Mine uses the native U-B in
GROMACS. My documentation (such as it is) does note this.
> My colleague is using some non-standard charmm parameters,
> so I also used the scripts from the gromacs site to convert our
> parameter files to gromacs format and included them in ffcharmm. I
> believe that I have done everything correctly, but I want to check that
> the energy of a given snapshot is the same when calculated by gromacs as
> it is in NAMD (which reads the charmm files directly). Most energies are
> looking close enough to be rounding errors, but my angle energy is off.
> I suspect that the distance restraint energy plus the angle energy will
> be the same as the angle energy as stated by NAMD, but I do need to be
> sure here. I don't see any indication of the distance restraint energy
> in the .log file or by g_energy.
Caveat that I haven't tested with GROMACS 4.0 yet, if you're using my
stuff correctly, then there will be an explicit U-B term. If you're not,
then I can only guess what you've done wrong. Either you're actually
using Yuguang's version and not using some -DDISRES correctly, or you
are using mine but ignoring some warnings and/or not applying the Perl
> I know others have been using the charmm forcefield, and I am wondering
> how they solved this problem. Perhaps I have done something incorrectly,
> but if the distance restraint energy is in fact not accessible, then
> this is also a suggestion to include that in the .edr file for gmx 4.1.
Distance restraint energies do get written when they are present. I
think the issue here is that they are not present.
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