[gmx-users] zero charge model- simulation time

[Justin A. Lemkul]

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?

-Justin

> Regards,
> 
> On 28 July 2011 12:54, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://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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> 
> 
> -- 
> Thanks,
> Jennifer N.
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================