sorry Justin to get back to you gain. This means I have to set zero charges twice ( after grompp EM and grommp MD), since in grompp_md I am using topology file which sets actual charges again to all atoms. Do atoms charges affect EM configuration ?<br>
<br>Regards,<br><br><div class="gmail_quote">On 28 July 2011 17:44, 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 class="im"><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 Justin,<br>
<br>
I am using tpbconv to set zero charges after em and after doing grompp_md.<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>
Do I need to use tpbconv after grompp_em? (before mdrun_em)<br>
<br>
</blockquote>
<br></div>
If you want to do energy minimization with zero charges, then yes.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards,<div><div></div><div class="h5"><br>
<br>
On 28 July 2011 14:53, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Juliette N. wrote:<br>
<br>
Hi again,<br>
<br>
I am wondering if using tpbconv to set zero charges (case 1)<br>
works similar to when one sets zero atom charges in topology<br>
file from the very beginning (case 2). Do these two cases work<br>
similarly?<br>
<br>
<br>
They should work identically.<br>
<br>
<br>
I checked tpr file and I see that charges are set to zero.<br>
<br>
Can you please tell me what these lines mean?<br>
<br>
Does it refer to exclusion which is set to 3 in top file?<br>
<br>
<br>
Yes.<br>
<br>
<br>
excls[0][0..10]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10}<br>
excls[1][11..18]={0, 1, 2, 3, 4, 5, 6, 7}<br>
<br>
The number of these lines corresponds to atom numbers in the system.<br>
<br>
<br>
They refer to the atom indices of the atoms in the [moleculetype],<br>
not the consecutive numbering of the system (for the first molecule<br>
this will be the same, but I thought I'd point that out).<br>
<br>
<br>
-Justin<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></div></div>
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</div></blockquote><div><div></div><div class="h5">
<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>
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