[gmx-users] RMSD per residue

[Justin Lemkul]

On 12/19/13 6:03 AM, Saman Shahriyari wrote:
> Dear users I am trying to have the "RMSD per residue" profile of my
> trajectory. i approached this by using "g_rmsf" tool with "-od" and "-res"
> options. although i can have such profile, but it seems that the average
> structure of my trajectory is being chosen as the reference to measure
> deviations from. if it is the case, is there any way i can use the starting
> structure of trajectory as the reference structure to have a profile of RMSD
> pre residue by g_rmsf tool (or any other tool)? in fact I am trying to know
> how much of deviation each residue has experienced through the simulation
> time.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2010-February/048889.html

Fitting should be done against the structure in the .tpr file.  It is easy to 
test this by compiling a new .tpr file with a different configuration.  If 
fitting is being done to the average structure in the trajectory, the answer 
will not change.  If fitting is being done to the structure in the .tpr file, 
the answer will change.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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