On 4/03/2011 4:53 PM, גדעון לפידות wrote:
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?
Thanks,
Gideon
This is normal and correct behaviour. There is no way to design the code
so that all users' analysis and visualization wishes can be anticipated
during the simulation. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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