[gmx-users] to gro or not to gro

[chris.neale at utoronto.ca]

It's more useful if you provide more information. What was the .pdb  
file (can I download it from the pdb databank?) was there water? what  
version of gromacs? was it compiled in double or single precision?  
what were your mdp parameters?

-- original message --

There is something not quite right here.

I grompp a gro file created from a pdb file using pdb2gmx and run MD to do
a single point energy calculation.

I then grompp the original pdb file and run MD to do a single point energy
calculation.

The values of potential energy values are different by about 3 kJ/mol for a
small molecule.

These things should carry a "bad for your health" sign :D