Re: colvars with replica exchange molecular dynamics

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jan 30 2014 - 17:32:47 CST

If I understood correctly your email, some restart files are not correctly
written before an exchange between replicas occurs. I assume that
"replicaBarrier" is there and that T-REMD without a colvars configuration
happens correctly, right?

On Thu, Jan 30, 2014 at 5:38 AM, Francesco Pietra <chiendarret_at_gmail.com>wrote:

> 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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