<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV></DIV>
<DIV>Hi,</DIV>
<DIV> </DIV>
<DIV>For average distance, you can gather distance v. time by g_mindist, then average them.</DIV>
<DIV> </DIV>
<DIV>For "average energy", you are refering to interaction energy? What you can do is to define two energy groups for two residues separatedly, make a new tpr and use mdrun rerun to get it.</DIV>
<DIV> </DIV>Regards,<BR>Yang Ye
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"><BR><BR>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: MoJie Duan <mjduan@smail.hust.edu.cn><BR>To: gmx-users@gromacs.org<BR>Sent: Sunday, October 7, 2007 10:49:26 PM<BR>Subject: [gmx-users] How to calculate the average distance or energy between two residues?<BR><BR>Hi, everyone!
<P style="MARGIN: 0cm 0cm 0pt 0pt">
<P style="MARGIN: 0cm 0cm 0pt 0pt">
<P style="MARGIN: 0cm 0cm 0pt 0pt">I want to calculate the average energy (like vdw potential) and average distance between two residues (or two atoms) during a simulation process, how can i do this? Is there any exist package?
<P style="MARGIN: 0cm 0cm 0pt 0pt">
<P style="MARGIN: 0cm 0cm 0pt 0pt">
<P style="MARGIN: 0cm 0cm 0pt 0pt">best wishes!</P></DIV><BR></DIV></div></body></html>