<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>So the problem is that .tpr file has peptide shifted in another box as after g_rms with -pbc option, RMSD is still ~1.5A => .tpr file generated from .mdp file during grompp programme, has peptide away from its usual position. I am giving pbc = xyz in .mdp file as well. Why then .tpr file should have peptide displaced ?<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br>Regards,<br>Nikhil<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 12:28:05 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Hello<br></font><br>nikhil damle wrote:<br>> 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.<br><br>So? You need to compare that with pre-simulation...<br><br>> 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>Try trjconv like my link suggested.<br><br>Mark<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><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a
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