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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Jul 28 02:45:58 CEST 2009

What hydrogen did you use? Without substantially more cut and paste on  
your end I am in the dark and can't help very much.

On the side, I'll mention that your sigma, and especially your  
epsilon, looks very low here. I'm no gold expert though, and I am just  
pointing that out even though that is not likely to be the source of  
your problem.

  AG         AG     47   107.8700     0.000       A    2.80455e-01  1.73304e-01

I believe that I also asked for your ffoplsaa.itp file. Is your  
comb-rule set correctly? Are you sure that you are getting the  
ffoplsaanb.itp inclusion that you intend? For example, I use

[ defaults ]
; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
1		3		yes		0.5	0.5

#include "/home/cneale/gromacs/oplspope.top/ffoplsaanb.itp"
#include "/home/cneale/gromacs/oplspope.top/ffoplsaabon.itp"

in my modified ffoplsaa.itp where the directories are hard coded to  
ensure that I get what I expect (rather than some unmodified  
ffoplsaanb.itp from $GMXLIB)

I can't think of anything else. You need to send a lot more data to  
this list. I am currently working under the assumption that you have  
made a mistake somewhere, and thus also assume that one of your  
descriptive statements is either misleading or incorrect -- hence the  
need for seeing the actual files (on list please). If, on the other  
hand, you are sure that you have done everything correctly then I  
can't help.

Good luck,

-- original message --

Here are some more details:

My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.

I could also add that each Ag belongs to its own charge group, so they
should be "felt".
I've tried starting with a different geometry as well with similar results.

Files were modified as follows:

ffoplsaa.atp  I added Silver as:

  AG        107.87

ffoplsaanb.itp  I've added:

  AG         AG     47   107.8700     0.000       A    2.80455e-01  1.73304e-01

Chris Rowan

More information about the gromacs.org_gmx-users mailing list