From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 30 2014 - 04:38:47 CST
Hi Giacomo:
I forgot to mention that I was using namd2.10. However, in the recent past,
same issue with namd2.9 on the same BlueGene/Q
francesco pietra
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Jan 29, 2014 at 5:40 PM
Subject: Fwd: namd-l: colvars with replica exchange molecular dynamics
To: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>, NAMD <namd-l_at_ks.uiuc.edu>
Hi Giacomo:
Back to BluegeneQ for T-REMD with colvars. I carried out other debug runs
with the same system of peptide under GB, non periodic, 32 replicas, temp
interval 300-600K.
job0 (with standard replica.namd file) was carried out correctly, rmsd
colvars
...............................
rmsd {
atoms {
# add all the C-alphas within residues 41 to 48 of segment "P1"
psfSegID P1
atomNameResidueRange CA 41-48
}
refPositionsFile npt-01_autopsf.pdb }
}
# apply harmonic potential to the "rmsd" variable
# with center on zero
# colvars and centers should both be lists, appearing only once in the block
harmonic {
name P2i_harmonic
colvars { colvar1 }
centers 0.0
forceConstant 100.0
}
...................................
being transferred into each replica for restarting, such as for replica 0:
fold_P2i.job0.0.colvars.state
The folder /output contains the file "fold_P2ijob0.restart.100.tcl", which
reads:
...........................
set i_job 1
set i_run 100
set i_step 10000
set restart_root output/%s/fold_P2i.job0.restart100
.......................
i.e., for restarting with job1, but without anything about colvars.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
On restarting with job1, I added colvarsInput to replica.namd, in analogy
to indications for umbrella sampling, as follows;
.....................
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
}
............................
The error is now clear, in the sense that it occurs on all replicas, for
example replica 17 log file ends with:
................................................
colvars: Initializing a new "harmonic" instance.
colvars: # name = P2i_harmonic
colvars: # colvars = { colvar1 }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 100
colvars: # centers = { 0 }
colvars: # targetCenters = { 0 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
colvars: # outputAccumulatedWork = off [default]
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Error: in opening restart file
"output/17/fold_P2i.job0.restart100.17.colvars.state".
colvars: If this error message is unclear, try recompiling with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
................................................
The same for other replicas, with their specific number in place of 17.
certain replicas ended at "colvars: Collective variables biases
initialized, 1 in total." just before the message of error. Showing the
error or not occurs randomly.
The little I can understand is that the trick I used does not pass
correctly the information about colvarsInput to the system. Standard
replica.namd does not work at all for restarting a T-REMD with colvars.
Ask me please any other information about what I did, or suggest what I
could try in addition.
Thanks
francesco pietra
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Jan 14, 2014 at 9:25 AM
Subject: Re: namd-l: colvars with replica exchange molecular dynamics
To: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Cc: NAMD <namd-l_at_ks.uiuc.edu>
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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