[gmx-users] Probelm of g_rms

[nikhil damle]

Yes. I am correcting the trajectory for periodicity

Regards,
Nikhil




________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, 23 September, 2009 3:48:47 PM
Subject: Re: [gmx-users] Probelm of g_rms



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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