[gmx-users] Accessing the distance_restraints energy term
chris.neale at utoronto.ca
Mon Dec 1 19:27:53 CET 2008
Thanks Mark for your assistance.
I have discovered the source of my problems in getting distance_restraints working.
Without disre=simple in the mdp file, disre=no is assumed and, according to the manual:
"no distance restraints (ignore distance restraint information in topology file)"
While I admit that this information was readily available to me, it is so counter-intuitive to me
that a defined distance restraint would simply be ignored that I am posting the solution here
in case anybody else gets confused on this topic.
-- original message --
/>/ 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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