[gmx-users] Re: Re: g_rmsf reference structure? (Tsjerk Wassenaar)

[kulleperuma.kulleperuma at utoronto.ca]

Thank you very much for the clarification!

>
> Message: 1
> Date: Wed, 16 Feb 2011 10:46:18 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] g_rmsf reference structure?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<AANLkTi=6-RMt6k+kz1+qpFSA-OttgFpirY5+EppV+jbb at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> The reference is used for fitting. The RMSF is calculated with respect
> to the average (fitted) structure, unless you explicitly specify that
> deviations from the reference should be used.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham   
> <Mark.Abraham at anu.edu.au> wrote:
>> On 16/02/2011 3:44 PM, kulleperuma.kulleperuma at utoronto.ca wrote:
>>>
>>> Dear all,
>>>
>>> I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms
>>> with reference to the average structure between 5-10 ns of a total of 10 ns
>>> simulation as below;
>>> g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 10000 ?o rmsf.xvg
>>>
>>> My understanding of the RMSF is as follows;
>>>
>>>  RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)
>>>
>>> where T is the time over which one wants to average, and Xi is the
>>> reference position of particle i, which is the time-averaged   
>>> position of the
>>> same particle i.
>>> What I am confused is whether g_rmsf takes the reference structure from
>>> the structure file (-s), which in my case, the md.tpr and NOT the time
>>> averaged position over the specified time?
>>
>> It does take the reference structure from -s. Whether you actually want the
>> RMSF from the non-physical time-averaged structure is up to you. IIRC you
>> might be able to get such an average from g_cluster.
>>
>> Mark
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
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> End of gmx-users Digest, Vol 82, Issue 126
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