[gmx-users] disparity in RMSD calculation

X Rules xrules at live.com
Sat Nov 20 09:39:17 CET 2010

I have had a similar experience, I have not investigated it thoroughly at the moment, but I get different (identical with specific jumps possibly due to pbc) plots if I take starting structure as my input pdb file or if my starting structure is first structure of trajectory. 

I think the plots would be fine if you just use g_rms -s topol.tpr -f traj.xtc 

> Date: Sat, 20 Nov 2010 19:05:35 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] disparity in RMSD calculation
> On 20/11/2010 4:54 PM, Sunita Patel wrote:
> > Dear Users,
> >
> > I calculated RMSD for a trajectory with same reference structure using GROMACS
> > and VMD. I observed completely difference plots for the same data. Please see
> > the attached file.
> >
> > What could be the cause for this disparity?
> >
> We can't be definitive without more detail of your two methods. The 
> jumps look like differing PBC treatments. See trjconv -h for ways to 
> choose how they are treated. Note that the "non-jumped" parts of the 
> GROMACS curve agree with the VMD one.
> Mark
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