Hello Justin,<br><br>I am using tpbconv to set zero charges after em and after doing grompp_md. <br><br><p style="border: medium none; text-align: justify; padding: 0cm;"><font size="2"><span style="font-family: 'Book Antiqua','serif';">grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr</span></font></p>
<p style="border: medium none; text-align: justify; padding: 0cm;"><font size="2"><span style="font-family: 'Book Antiqua','serif';" lang="DE">tpbconv –s </span><span style="font-family: 'Book Antiqua','serif';"></span><span style="font-family: 'Book Antiqua','serif';">*_md.tpr</span><span style="font-family: 'Book Antiqua','serif';" lang="DE"> -o </span><span style="font-family: 'Book Antiqua','serif';">*-ZERO</span><span style="font-family: 'Book Antiqua','serif';">_md</span><span style="font-family: 'Book Antiqua','serif';" lang="DE">.tpr –zeroq</span></font></p>
<p style="border: medium none; text-align: justify; padding: 0cm;"><font size="2"><span style="font-family: 'Book Antiqua','serif';" lang="DE">mdrun </span><span style="font-family: 'Book Antiqua','serif';"></span><span style="font-family: 'Book Antiqua','serif';" lang="DE">-s </span><span style="font-family: 'Book Antiqua','serif';" lang="DE"></span><span style="font-family: 'Book Antiqua','serif';">*-ZERO</span><span style="font-family: 'Book Antiqua','serif';">_md</span><span style="font-family: 'Book Antiqua','serif';" lang="DE"> -o -c -e -x -v</span></font></p>
Do I need to use tpbconv after grompp_em? (before mdrun_em)<br><br>Regards,<br><br><div class="gmail_quote">On 28 July 2011 14:53, 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;">
Hi again,<br>
<br>
I am wondering if using tpbconv to set zero charges (case 1) works similar to when one sets zero atom charges in topology file from the very beginning (case 2). Do these two cases work similarly?<br>
<br>
</blockquote>
<br></div>
They should work identically.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
Yes.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
They refer to the atom indices of the atoms in the [moleculetype], not the consecutive numbering of the system (for the first molecule this will be the same, but I thought I'd point that out).<div class="im"><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></div><div><div></div><div class="h5">
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>
==============================<u></u>==========<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Thanks,<br>J. N.<br><br>