nikhil damle wrote:
Hi all,
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 ?
Are you correcting the trajectory for periodicity?
-Justin
Regards,
Nikhil
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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