colvars with replica exchange molecular dynamics

From: Francesco Pietra (
Date: Mon Jan 13 2014 - 14:29:41 CST

Some time ago I asked much this same question which must have gone lost or
anyway raised no interest. Nonetheless, the issue is at the heart of
carrying out t-remd while restraining a portion of the molecule with

Setting colvars in namd config file for remd

# constraints
colvars on
colvarsConfig ./

gives correct

in all replicas and a restart file in /output folder. This restart file
does not provide any information about colvars. My question is where
information about colvars is provided. I can't see any.

For umbrella sampling it is advised to add a line to the guiding file

colvarsInput $restart_root.$replica_id.colvars.state

to elicit information about colvars. On this basis, I added the same line
to replica.namd, as shown below:

if {$i_run} { #restart
  bincoordinates $restart_root.$replica_id.coor
  binvelocities $restart_root.$replica_id.vel
  extendedSystem $restart_root.$replica_id.xsc
  colvarsInput $restart_root.$replica_id.colvars.state
} else {
  temperature $NEWTEMP

It did hot help; the .err file told that:

REPLICA 23 FATAL ERROR: Error in the collective variables module: exiting.

The replica 23 log file, tells that:

colvars: Collective variables biases initialized, 1 in total.fold_P2i.job0.
colvars: Error: in opening restart file

The conclusion is that a t-remd with colvars cannot be properly restarted
as far as I can understand. Probably most t-remd simulations are carried
out without colvars, but there are situations where restraints on a portion
of the molecule are needed.

Thanks for your attention

francesco pietra

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