Dear all,
I have a problem concerning bonds in sander. I set up a MD-Simulation of
EMIM/FSI and the intermolecular results are good but intra molecular
results are very bad so I decided to simulate one single molecule. The
simulation is running but sander assign wrong bond parameter to the
bonds. I attached my input data. I erase nonbonded and charge parameters
to localize the problem but the problem is still there. For bonds
between S and N there are different values in may analysis but the
prmtop looks right. My cubicle neighbour also tries this and analyses it
and get the same results. Has anyone an idea what is wrong? I'm confused
because if I delete the lone pair everything works fine.
Thanks for your support,
Volker
--
Volker Lesch
Institut für physikalische Chemie
Westfälische Wilhelms-Universität Münster
Corrensstrasse 28/30
48149 Münster
Phone: +49-(0)-251-83-29180
Email: volkerlesch.uni-muenster.de
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 14 2013 - 07:00:02 PST
