<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>Yes. I am correcting the trajectory for periodicity<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> Justin A. Lemkul <jalemkul@vt.edu><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> Wednesday, 23 September, 2009 3:48:47 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Probelm of g_rms<br></font><br><br><br>nikhil damle wrote:<br>> Hi all,<br>> <br>> I am facing the problem
while calculating backbone RMSD over 30 ns. upto ~6-7 ns g_rms gives correct RMSDs and later all RMSD values are unexpectedly and unusually high (within 20 ps RMSD value shoots up by ~8A). But when i calculate RMSD using g_confrms programme, it gives me expected and usual RMSD. I tried running g_rms separately for that particular time range which was giving me high values only to get same result once again. Is there problem with g_rms or i am calculating wrongly ?<br>> <br><br>Are you correcting the trajectory for periodicity?<br><br>-Justin<br><br>> Regards,<br>> Nikhil<br>> <br>> ------------------------------------------------------------------------<br>> Connect more, do more and share more with Yahoo! India Mail. Learn more <<a href="http://in.rd.yahoo.com/tagline_galaxy_3/*http://in.overview.mail.yahoo.com/" target="_blank">http://in.rd.yahoo.com/tagline_galaxy_3/*http://in.overview.mail.yahoo.com/</a>>.<br>> <br>>
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========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (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 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 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 www interface or send it
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