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 <jalem...@vt.edu
<mailto:jalem...@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
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