[gmx-users] zero charge model- simulation time

Juliette N. joojoojooon at gmail.com
Thu Jul 28 19:11:24 CEST 2011

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.

I am concerned about the model to be inaccurate. Do these two models work


On 28 July 2011 12:54, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Juliette N. wrote:
>> Hello,
>> 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            =  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.
> 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
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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Jennifer N.
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