[gmx-users] disparity in RMSD calculation

[Sunita Patel]

With topol.tpr file, am getting identical plot as that of VMD.
Thanks,
Sunita

On Sat, 20 Nov 2010 08:39:17 +0000, X Rules wrote
> 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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Dr. Sunita Patel 
--------------------------------------------- 
Visiting Fellow 
Department of Chemical Sciences 
T.I.F.R., Homi Bhabha Road, Colaba 
Mumbai - 400005 
---------------------------------------------
 
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