[gmx-users] zero charge model- simulation time
joojoojooon at gmail.com
Thu Jul 28 18:47:14 CEST 2011
I set zero charges to all atoms using the commands below:
grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr
tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq
mdrun -s *-ZERO_md -o -c -e -x -v
So before doing mdrun md I add tpbconv command and use the out put
for the mdrun md step.
I did not touch mdp file to exclude
rcoulomb-switch = 0
rcoulomb = 1.0
Although g_Energy is giving zero values for coulomb SR and 14 terms, CPU
time doesnt change for the models with and without charges.
I am just curious why run time is not changing given that electrostatics is
the most time consuming calculation. Do I need to remove above lines from
mdp? I am doubtful if electrostatic has been ignored from my model.
Please let me know your ideas.
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