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<DIV>A more complete answer is that to define energy groups for this reside and rest residues respectively, generate the tpr with grompp and then use mdrun -rerun to run through the existing trajectory to obtain what you wanted.<BR> </DIV>Regards,<BR>Yang Ye
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<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif">----- Original Message ----<BR>From: Justin A. Lemkul <jalemkul@vt.edu><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Monday, September 1, 2008 5:37:47 AM<BR>Subject: Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?<BR><BR><BR><BR>Limei Zhang wrote:<BR>> Dear all,<BR>> <BR>> <BR>> <BR>> Is it possible to use GROMACS function(s) to calculate the averaged van <BR>> der Waals potential /Coulomb potential between a given residue and the <BR>> rest residues in the protein during a certain time of simulation?<BR>> <BR>> <BR><BR>Different contributions to the potential can be analyzed by specifying the <BR>appropriate 'energygrps' in the .mdp file.<BR><BR>-Justin<BR><BR>> <BR>> Thanks,<BR>> <BR>> <BR>> <BR>>
LZhang<BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> <BR>> _______________________________________________<BR>> gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php"
target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR><BR>-- <BR>========================================<BR><BR>Justin A. Lemkul<BR>Graduate Research Assistant<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.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>_______________________________________________<BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before
posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR></DIV></DIV></div></body></html>