From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jan 13 2014 - 15:17:25 CST
Francesco, is this a reproducible error, i.e. is it always replica 23 which
gives you the error message?
On Mon, Jan 13, 2014 at 3:29 PM, Francesco Pietra <chiendarret_at_gmail.com>wrote:
> 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
>
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