From: Francesco Pietra (chiendarret_at_gmail.com)
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
colvars.
Setting colvars in namd config file for remd
# constraints
colvars on
colvarsConfig ./P2i_rmsd-colvars.in
gives correct
fold_P2i.job0.0.colvars.state
fold_P2i.job0.0.colvars.traj
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.
restart500.23.colvars.state
colvars:
----------------------------------------------------------------------
colvars: Error: in opening restart file
"output/23/fold_P2i.job0.restart500.23.colvars.state".
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
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:02 CST