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

Chris Neale chris.neale at utoronto.ca
Mon Jul 27 21:49:02 CEST 2009

what's your minimum atomic distance achieved between Ag and your other molecule (g_mindist)? 

If it's < 0.09 nm then you definitely do have some error in your setup. For proof of that, generate a new system that is identical to yours
but this time use only standard OPLS atom-types and see the problem likely disapear.

If not, then the penetration is just because it goes between atoms and in this case, while you may not have an "error" per se, 
you should check your parameters and possibly your assumptions about what should be happening.

Also, it's very difficult to offer advice when you describe a problem without showing some of the important files directly.
Can you paste the changes to your .itp files and the ffopsaa.itp main file that you are using?

Hi Chris,

-- original message --

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?

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