Re: problem restarting multiple walker metadynamics

From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Thu Mar 12 2015 - 17:26:10 CDT

To clarify- the initial simulation was done for 7.5ns per replica, so this
corresponds to ~300 kcal/mol of external potential being added over a total
of 210ns. My apologies for not making this clearer in the original message!
- Amy

On Wed, Mar 11, 2015 at 10:49 PM, Amy Rice <arice3_at_hawk.iit.edu> wrote:

> As far as I can tell, there were no instabilities along the way. There
> were no error messages reported, and the pmfs generated by each replica
> appear to align. Additionally, all 28 replicas ended normally after 7.5 ns
> and generated the expected files (coor, vel, dcd, colvars.state,
> colvars.traj, etc.). Is there anything else I can check to verify that
> there were no instabilities in the initial run?
> Thank you for the response,
> - Amy Rice
>
> On Wed, Mar 11, 2015 at 6:29 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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/
>>
>>
>
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
>

-- 
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology

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