[gmx-users] Probelm of g_rms

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 23 12:18:47 CEST 2009

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?


> 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


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