[gmx-users] REg MD results

[Justin Lemkul]

On 1/10/17 3:07 AM, Parul Raj Srivastava wrote:
> Dear Sir,
>
> On analysing each chain separately,though the rmsd is stable but the rmsf
> is not beginning from the origin and suddenly rising from the centre of
> falling off towards the end.
>

RMSF is a per-residue quantity, not a time series.  There's no reason to expect 
it to start at the origin of the plot.  If a residue has an RMSF of zero, it 
never moved.

-Justin

> Regards,
> Parul Raj Srivastava,
> M.Tech.Computational Biology,
> Anna University,Chennai-600025
>
> On Sun, Jan 8, 2017 at 1:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 1/7/17 5:14 AM, Parul Raj Srivastava wrote:
>>
>>> I have given an MD run for a quaternary protein structure by taking 2
>>> chains at a time for the MD run.The rmsf graph so obtained is showing
>>> erratic behaviour,please find attached graph.Is this result justified or
>>> incorrect??
>>>
>>>
>> The list does not accept attachments.  If you want to share an image,
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>>
>> Often it is just easier to create index groups for each chain and analyze
>> them separately.  This eliminates most confusion associated with
>> residue-specific analyses like RMSF.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================