[gmx-users] simulation crash with GROMOS96 force field

Chris Neale chris.neale at utoronto.ca
Sun Jan 24 20:50:36 CET 2010

Dear Vitaly:

1. No problem at all in vacuo? That with a 1 fs timestep and the sd 
integrator? Strange then that your molecule is ok and the water is ok, 
but they are unstable together. Perhaps your'e not getting any LJ 
interactions (or not correct ones) between your solute and water? That's 
where I would focus my efforts if I was you. I suppose it could also be 
solute-solute LJ problems...

2. Certainly not. You can't simply remove parameters just because it 
crashes when you have them.

-- original message --

 > 1. put a single solute in a large vacuum box and use the sd
 > integrator. Can you reproduce the problem?

No problem in vacuo found.

 > 2. Remove the dihedral parameters entirely. Can you reproduce the 

The problem appeared between carbon and hydrogen 1-4 atoms... Would
you advise to remove them from [pairs] section?


More information about the gromacs.org_gmx-users mailing list