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. <br><br>I am concerned about the model to be inaccurate. Do these two models work similarly? <br>
<br>Regards,<br><br><div class="gmail_quote">On 28 July 2011 12:54, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Juliette N. wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello,<br>
<br>
I set zero charges to all atoms using the commands below:<br>
<br>
grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr<br>
<br>
tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq<br>
<br>
mdrun -s *-ZERO_md -o -c -e -x -v<br>
<br>
So before doing mdrun md I add tpbconv command and use the out put *-ZERO_md.tpr for the mdrun md step.<br>
<br>
I did not touch mdp file to exclude<br>
<br>
coulombtype = <br>
rcoulomb-switch = 0 rcoulomb = 1.0 <br>
Although g_Energy is giving zero values for coulomb SR and 14 terms, CPU time doesnt change for the models with and without charges. <br>
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.<br>
<br>
</blockquote>
<br></div></div>
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).<br>
<br>
The only way to exclude these interactions is to use energygrp_excl, but that will exclude all nonbonded interactions, not just the electrostatics terms.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Thanks,<br>Jennifer N.<br><br>