From: Joshua Adelman (jla65_at_pitt.edu)
Date: Fri Nov 18 2011 - 14:21:46 CST
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?
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.
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