Re: restart with constraints causes RMSD "jump"

From: P.-L. Chau (
Date: Wed May 25 2011 - 12:56:41 CDT

Thank you for your prompt reply.

> The coordinates used for the constraints are being overwritten by the
> bincoordinates file. You can see this because the BOUNDARY energy where
> constraints are reported is zero at restart. This only happens if the
> coordinates and consref filenames are the same, so you can work around
> the issue by giving the files different names (or make one a symlink to
> the other). I just checked in a fix that moves the bincoordinates read
> to after constraints reference coordinates have been copied.

I am new to NAMD so could I follow up with two questions, please? If you
do not mind, could I possibly start from the beginning?

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?

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?

I am sorry if these questions sound idiotic, but I am a new user so I beg
you to bear with me. Thank you for your kind help and advice.

P-L Chau

Bioinformatique Structurale
Institut Pasteur
75724 Paris

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