[gmx-users] Accessing the distance_restraints energy term

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 6 04:42:34 CET 2008

chris.neale at utoronto.ca wrote:
> Hello,
> 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 
> potentials.

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 
scripts correctly.

> 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.


More information about the gromacs.org_gmx-users mailing list