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,
Chris
-- 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
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