[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...

Christopher Rowan chriskrowan at gmail.com
Mon Jul 27 21:41:24 CEST 2009

Hi Chris,

I've done a gmxdump and there aren't any zeros for any of the LJ values.
No capital letter problems either.

Chris Rowan

Mon, 27 Jul 2009 12:30:54 -0700

Sounds like your topology/forcefield is incorrect or incomplete.

Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate
that you don't have any LJ parameters for
some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters
by hand. Are there any zero's where you should have numbers?
Perhaps you mixed up some atom types (e.g. with capitilization) or you simply
didn't add the necessary values.


-- original message --


I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file.  My system topology I've
written by hand in an itp file.  The problem is that after any kind of run
the molecule penetrates the metal surface!  This shouldn't be happening.  I
had been using g45a3 quite successfully for the same system and everything
was working fine.  Do I need to do something different/special with oplsaa?
What am I missing?

Advice appreciated,
Chris Rowan

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