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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 4 07:24:44 CET 2011

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 


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