[gmx-users] zero charge model- simulation time

Juliette N. 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

coulombtype         =

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.

Thank you,
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