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<DIV><FONT face=Arial size=2>Hi Maarten</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Perhaps with g_cluster.</FONT></DIV>
<DIV><FONT face=Arial size=2>If the protein doens't have large conformational
changes during your simulation, I think you could do clustering of the run, and
if I'm not mistaken, g_cluster has an option to spill out the average structure
and/or the central structure of each found cluster.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Best regards,</FONT></DIV>
<DIV><FONT face=Arial size=2>Nuno</FONT></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=maarten_wolf@yahoo.co.uk
href="mailto:maarten_wolf@yahoo.co.uk">Maarten Wolf</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Thursday, September 16, 2004 12:05
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] calc. average
protein structure</DIV>
<DIV><BR></DIV>
<DIV>Hello,</DIV>
<DIV> </DIV>
<DIV>Does anyone know how I can compute/calculate the average structure
of my protein after an md simulation?</DIV>
<DIV> </DIV>
<DIV>Thanks in advance,</DIV>
<DIV>Greetings,</DIV>
<DIV> </DIV>
<DIV>Maarten Wolf</DIV>
<DIV>TuDelft</DIV>
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