<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>I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ??<br><br>Regards,<br>Nikhil<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><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> Tuesday, 14 July, 2009
12:07:24 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Hello<br></font><br>nikhil damle wrote:<br>> I am carrying out energy minimization of the protein peptide complex. But even after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide far away from the binding site. This did not happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar .mdp file is given for energy minimization. What could be possible reasons for such flying away of the peptide ? How should I fix the problem ?<br><br>Please use a descriptive subject line, not a generic greeting.<br><br>You are probably seeing a periodicity artefact. See <a href="http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions" target="_blank">http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions</a><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a
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