Re: restart with constraints causes RMSD "jump"

From: Jim Phillips (
Date: Wed May 25 2011 - 13:40:21 CDT

On Wed, 25 May 2011, P.-L. Chau wrote:

> If I run a simulation sim1 of a protein using files protein.pdb and
> protein.psf, then sim1.conf should have two lines like these:
> structure protein.psf
> coordinates protein.pdb
> so that the coordinates used for starting the run is protein.pdb.
> If I would like to restart from the end of sim1 to run sim2, then in the
> sim2.conf file, I usually have a few lines like these:
> structure protein.psf
> coordinates protein.pdb
> bincoordinates sim1.restart.coor
> binvelocities sim1.restart.vel
> extendedsystem sim1.xsc
> Could I ask you if the line "coordinates protein.pdb" is necessary? If the
> starting coordinates is already defined to be sim1.restart.coor, then why
> do we need protein.pdb, please?

With the current code you must specify a coordinates PDB file even if
you're also providing a binary coordinates file. There is no reason this
requirement could not be eliminated in a future version, although it would
still be required if you wanted (for whatever reason) to read binary
coordinate files but write PDB output or restart files.

> The second question pertains to the constraints. I put constraints on
> using the following lines:
> constraints on
> consexp 2
> consref protein.pdb
> conskfile protein100.cnst
> conskcol B
> margin 3
> You wrote that I should NOT have "consref protein.pdb" and "coordinates
> protein.pdb", is that right? So if I copy protein.pdb to protein_ref.pdb
> and use the latter as the consref file, then would this "jump" disappear?

Yes. You could also (assuming Linux) ln -s protein.pdb protein_ref.pdb.


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