[gmx-users] Dimer g_rms

XAvier Periole x.periole at rug.nl
Wed Jun 30 10:58:26 CEST 2010

On Jun 30, 2010, at 10:34 AM, Carla Jamous wrote:

> Dear all,
> I'm running my first simulation of a dimer.
> When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha)  
> to get the RMSD of the whole dimer, the graph is ascending, till  
> reaching a value of 8 A.
> in this case, I take a .tpr file, a .xtc file and a .ndx file of the  
> whole dimer.
> However, when I run g_rmsd on Calpha, but this time, to get the RMSD  
> of one chain (one monomer), the graph is constant with value around  
> 1 A. and this for both chains, when taken alone.
> In this case, I take a .tpr file, a .xtc file and a .ndx file of the  
> monomer.
> So is this an error of using g_rms?
Well this is not an error. Evidently your monomers are stable  
and you dimer is not.
This might be result of either an actual deformation of the dimer or
one of your monomer is crossing the periodic boundaries and thereby
the rmsd is not representative.
try to trjconv your trajectory using the -pbc nojump and run g_rms  
> Thank you.
> Carla
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