[gmx-users] RMSD analysis during production MD

[Justin A. Lemkul]

Acoot Brett wrote:
> 
>  Dear All,
>  
> During a 1 ns production analysis (before it completes), I can analysis 
> the RMSD by "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" 
> without influence the normal calculation of the production analysis, right?
>  

It's always safer to make a copy of the trajectory and do any sort of operation 
on it.  I doubt that mdrun and g_rms would conflict as far as creating errors in 
the calculations themselves, but you may run into simple I/O trouble if you've 
got multiple processes trying to open/close a trajectory file at the same time.

-Justin

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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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