[gmx-users] g_rmsf reference structure?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Feb 16 10:46:18 CET 2011


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.



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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