[gmx-users] Probelm of g_rms

[Tsjerk Wassenaar]

Hi Nikhil,

Try extracting the frame just before and just after the jump and view
them in pymol/vmd/rasmol/... to check for a possible cause.

Cheers,

Tsjerk

On Fri, Sep 25, 2009 at 5:50 AM, nikhil damle <pdnikhil at yahoo.co.in> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623