[gmx-users] Which .tpr file to use for g_rms?

[Justin A. Lemkul]

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
> 

-- 
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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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