GROMACS version:
GROMACS modification: Yes/No
Hi,
I am trying to do some MD simulations of a protein interacting with a surface of muscovite mica. In order to do so, I generated a mica surface with CharmmGUI and modified the charmm27 forcefield (adapting the energy terms as there was some slight differences).
When I proceed with the preparation of the files I do not encounter any problems regarding how the forcefield is being read. The only strange thing is that when generating the simulation box, it does not automatically place the protein at the center (but I have had the same problem with other non-modified force fields). I understand that this can already be a sign of a problem, tho. Only when I start my energy minimization step, I get this error:
"Internal error (bug):
Step 0: The total potential energy is -nan, which is not finite. The LJ and
electrostatic contributions to the energy are -nan and -4.69549e+06,
respectively. A non-finite potential energy can be caused by overlapping
interactions in bonded interactions or very large or Nan coordinate values.
Usually this is caused by a badly- or non-equilibrated initial configuration,
incorrect interactions or parameters in the topology. "
I have tried to delete the water molecules that might be clashing with any atoms from either the protein or the mica surface, but I should not have to remove water molecules “clashing” with the protein atoms as the function solvate should take care of it, right?
Does anyone has an advice on how to proceed and try to solve this problem?
Thank you very much in advance!
PS: I attach the minim.mdp file, if other files are needed (I guess the modified force field, I can send those as well, just wasn’t sure how convenient would be to upload the full folder in the topic)
minim1.mdp (1.1 KB)