[gmx-users] Accessing the distance_restraints energy term

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Nov 6 04:05:54 CET 2008


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. 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.

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.


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