dur12 at psu.edu
Tue May 11 21:01:14 CEST 2010
Hi Gromacs Users,
I am trying to run a NVE simulation of a single dye molecule jumping
from state S0 to state S1. I have starting coordinates and velocities
from a previous NPT run of the same system at S0, however, the charges
are new, that of S1. I didnot generate any Maxwell-velocity for the NVE
run and followed the instructions that rlist should be ~0.3 nm larger
than rcoulomb and rvdw. I also increased Lincs_iteration value and the
table extension. Please note that I am using a tabulated interaction
potential for a particular dihedral.
The problem is, an increasing total energy during the NVE run and the
molecule collapses followed by segmentation fault. However, the S0-S1
jump sim runs fine in NPT ensemble.
Also, when I use null potential for the dihedral the NVE job runs fine.
Kind of confused and will really appreciate your help.
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