Anirban Ghosh wrote:
Hi ALL,
Its a very basic question but still...
When we calculate RMSD (or any other parameter) using the g_rms command,
we need to supply the .tpr file with -s option. Now suppose if I have a
total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there
will be 4 .tpr files. So at the end of 20 ns if I wish to calculate
RMSD, then which .tpr file should I suppy to g_rms, the first one or the
last one? We I run g_rms with the two .tpr files, I get different
results. So which one should be used? Any suggestion is welcome.
Use the one that contains the structure you wish to serve as your reference.
-Justin
Thanks,
Anirban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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