[gmx-users] RMSD analysis during production MD

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 25 01:28:18 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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