[gmx-users] RMSD from the average structure
tsjerkw at gmail.com
Thu Apr 25 22:36:03 CEST 2013
Hi Bipin Singh,
That indeed gives you the RMSD against the average. Do think about it a bit
more: do you want the average of the whole structure, or should you account
for a phase of relaxation?
On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/24/13 3:06 AM, bipin singh wrote:
>> Hi all,
>> Please let me know whether this is the right way to calculate RMSD from
>> average structure from a simulation:
>> g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
>> average.pdb: is the pdb file produced using -ox option of g_rmsf.
> You can calculate RMSD with respect to whatever structure you like, but
> the interpretation and justification for doing so are up to you.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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