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

[Mark Abraham]

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