From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jan 14 2014 - 02:25:19 CST
Giacomo:
Thanks so much for taking my post into consideration. That error message
was from a single t-remd with modified replica.namd. I need to run some
debugs in order to answer your question. That will take time if I move my
project from a BluGene with namd2.10 to a PLX machine with namd-cuda. I
read your answer as implying that our modification of replica.namd as for
umbrella sampling (suggested to me at CINECA) might be sound.
francesco
On Mon, Jan 13, 2014 at 10:17 PM, Giacomo Fiorin
<giacomo.fiorin_at_gmail.com>wrote:
> 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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