[gmx-users] different RMSD graphs after using pbc mol

גדעון לפידות glapidoth at gmail.com
Fri Mar 4 06:53:46 CET 2011

Hi all,
I was wandering if anyone knows of  a problem with gromacs 4.0.7 when it
comes to its RMSD tool. After running a 44 ns simulations on
a soluble protein I used g_rms to calculate RMSD . The results did not seem
to make sense ( >30 angstrom at some time points). After running pbc-mol and
center on the same xtc file and re-running the g_rms command, with the
exact same syntax I got a dramatic difference in RMSD results (no time point
>1 angstrom).
Has anyone else encountered such a problem?
And if so how can I correct it without modifying the xtc files?
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