[gmx-users] zero charge model- simulation time
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 28 19:30:05 CEST 2011
Juliette N. wrote:
> Thanks Justin. One last question, I wanted to make sure if zetting zero
> charge using tpbconv is identical to setting zero charges in top file.
Yes. Verify the contents of your .tpr file with gmxdump.
> I am concerned about the model to be inaccurate. Do these two models
> work similarly?
What two models?
> On 28 July 2011 12:54, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Juliette N. wrote:
> 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 *-ZERO_md.tpr for the mdrun md step.
> I did not touch mdp file to exclude
> coulombtype =
> rcoulomb-switch = 0 rcoulomb =
> Although g_Energy is giving zero values for coulomb SR and 14
> terms, CPU time doesnt change for the models with and without
> 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.
> Turning off charges will not improve performance. The MD routine
> will still calculate Coulombic interactions, but it will just waste
> time producing all zeros. The only difference you might be able to
> see would be PME vs. cutoff (the default coulombtype setting), with
> the latter being much faster (but also much less accurate).
> The only way to exclude these interactions is to use energygrp_excl,
> but that will exclude all nonbonded interactions, not just the
> electrostatics terms.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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> Jennifer N.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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