From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 11 2015 - 18:29:36 CDT
Did all the replicas in the first job conclude gracefully? I want to point
your attention to the fact that you have added 300 kcal/mol of external
potential in 7.5 ns, and I'm not sure there weren't any instabilities along
the way.
Giacomo
On Wed, Mar 11, 2015 at 8:59 PM, Amy Rice <arice3_at_hawk.iit.edu> wrote:
> Hi all,
> I am running multiple walker/well tempered metadynamics; I have 28 walkers
> and would ultimately like to run for 15ns each. Due to walltime
> limitations, I have to restart the simulation after 7.5ns, which is where
> the problem is occurring. After inspecting the pmfs generated after
> restarting, it seems to me that the colvar state information from before
> the restart is not being included, and that a new pmf is being generated
> instead. However, the log file shows that the colvars.state file is being
> read:
>
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables biases initialized, 1 in total.
> colvars:
> ----------------------------------------------------------------------
> colvars: Restarting from file "01/meta.KR12.colvars.state".
> colvars: Restarting collective variable "alpha" from value: 0.050172
> colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables module initialized.
> colvars:
> ----------------------------------------------------------------------
>
>
>
> Here is the relevant region of one of the restart configuration files:
>
> ------------------------------------------------------------------------------------
> structure KR12.ionized.psf
> coordinates KR12.ionized.pdb
> bincoordinates 01/meta.KR12.coor
> extendedsystem 01/meta.KR12.xsc
> binvelocities 01/meta.KR12.vel
>
> [....]
>
> #colvars
> colvars on
> colvarsConfig alpha01.in
> colvarsInput 01/meta.KR12
>
> -------------------------------------------------------------------------------------
>
>
>
> and one of the colvar configuration files:
>
> -------------------------------------------------------------------------------------
> colvarsTrajFrequency 5000
>
> colvar {
> name alpha
> width 0.005
>
> lowerboundary 0.0
> upperboundary 1.0
>
> lowerwallconstant 10
> upperwallconstant 10
>
> alpha {
> residueRange 19-28
> psfSegID P1
> }
> }
>
>
> metadynamics {
> colvars alpha
> hillWeight 0.5
> newHillFrequency 100
> hillwidth 2.5066
> wellTempered on
> biasTemperature 3000
> saveFreeEnergyFile on
> writeHillsTrajectory on
> multipleReplicas on
> ReplicaID 1
> replicasRegistry
> /oasis/scratch/arice3/temp_project/first/registry
> replicaUpdatefrequency 1000
> dumpPartialFreeEnergyFile on
>
> -------------------------------------------------------------------------------------
>
>
> Here is the final pmf generated before the restart (after 7.5ns):
>
> https://drive.google.com/file/d/0B2-4_f9dh-l2cllJa2QxaDZzQWc/view?usp=sharing
>
> The first three pmfs generated post-restart, same scale:
> (red is after 0.1ns of the restarted run, green is 0.2ns, and blue is
> 0.3ns)
>
> https://drive.google.com/file/d/0B2-4_f9dh-l2NzljbVZITzdlQ0U/view?usp=sharing
>
> Last pmf generated before the restart (pink/purple) and the first two
> after restarting (red and green):
>
> https://drive.google.com/file/d/0B2-4_f9dh-l2b3VDTDhDQ0Jsdjg/view?usp=sharing
>
> As I said, it seems to me that the information from before the restart is
> not being included. Is there a different way to restart multiple walker
> metadynamics runs, or perhaps an option that I neglected to include in my
> configuration files?
> Thank you for your help!
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
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