Re: RMSD trajectory

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sat Nov 19 2011 - 08:44:40 CST

Hi Joshua and Nikolaos.

Thanks for your help.

I think the best choice is pdb + dcd, 'cause the objective is to analyse how stable is the experimental structure along the time of simulation.

Best regards,

Flavio

--- On Fri, 11/18/11, Joshua Adelman <jla65_at_pitt.edu> wrote:

> From: Joshua Adelman <jla65_at_pitt.edu>
> Subject: Re: namd-l: RMSD trajectory
> To: "flavio seixas" <oivalf_nix_at_yahoo.com>
> Cc: "Namd l" <namd-l_at_ks.uiuc.edu>
> Date: Friday, November 18, 2011, 8:21 PM
> On Nov 18, 2011, at 3:09 PM, flavio
> seixas wrote:
>
> > Hi all.
> >
> > My question is: What is the best choice to calculate
> RMSD-trajectory plot for a simulation?
> >
> > The psf file plus the dcd file or the pdb file plus
> the dcd file?
> >
> > Or does not matter?
> >
> > Regards,
> >
> > Flavio
>
> Hi Flavio,
>
> Assuming that the pdb file is some initial model of your
> system that is essentially the experimental structure,
> you're potentially looking at two different things if your
> reference structure is the first frame loaded into VMD or
> whatever analysis software you're using:
>
> 1. pdb + dcd: This will give you the rmsd to there
> experimental structure
> 2. psf + dcd: This will give you the rmsd to the the first
> frame in the dcd
>
> It is possible that the first frame of the dcd is very
> close to the experimental structure and the difference will
> result in small differences in the output of your two
> scenarios. If however large deviations occurred during the
> minimization/heating/equilibration and your trajectory comes
> after that protocol, the answers could be different.
>
> The best choice depends on what you are looking to answer.
>
>
> Best wishes,
> Josh
>
>

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