<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear Elton,</span></div><div><span>Where am I supposed to use trjconv -center ? when I want to get the mdrun?</span></div><div> </div><div>Sincerely,<br>Shima<br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Elton Carvalho <eltonfc@if.usp.br><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, June 15, 2012 7:43 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] protein near the edges of simulation box<br>
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On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar <<a ymailto="mailto:tsjerkw@gmail.com" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>> You can specify the protein to have no net center of mass<br>> motion, by setting it as comm_grps in the .mdp file.<br>><br><br>If the user is just concerned about visualization, trjconv -center<br>solves his problem.<br><br>-- <br>Elton Carvalho<br>Tel.: +55 11 3091-6985/6922<br>Dept Física dos Materiais e Mecânica<br>Instituto de Física<br>Universidade de São Paulo<br>P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil<br>--<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
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