Thank you very much for the clarification!
Message: 1
Date: Wed, 16 Feb 2011 10:46:18 +0100
From: Tsjerk Wassenaar <[email protected]>
Subject: Re: [gmx-users] g_rmsf reference structure?
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
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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
<[email protected]> wrote:
On 16/02/2011 3:44 PM, [email protected] 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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