Re: [AMBER] combining trajectories with different parameter files

From: David A Case <>
Date: Mon, 14 May 2018 08:09:20 -0400

On Mon, May 14, 2018, Chetna Tyagi wrote:
> I have carried out different simulations of the same peptide with classical
> MD and accelerated MD. The parameter files that I used for these were
> different.
> Similarly, in chloroform solvent, I have used two different parameter files
> for some reason.
> Is it possible to strip the solvent from parameter files and combine these
> trajectories to analyze only the peptide and project it on the same PCA
> landscape?

Yes: PCA analysis doesn't depend on the force field parameters which
were used in the underlying trajectory: it just analyzes the
fluctuations in coordinates. So, if all the stripped trajectories have
the same number of atoms (in the same order), you should be fine.

Of course, if the force fields differ in significant ways, it may be
difficult to interpret the results you obtain.


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Received on Mon May 14 2018 - 05:30:03 PDT
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