Re: problem restarting multiple walker metadynamics

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 19 2015 - 18:39:06 CDT

Ok I'll look into the problem more closely.

Giacomo
On Mar 19, 2015 11:44 PM, "Amy Rice" <arice3_at_hawk.iit.edu> wrote:

> I have reproduced the restart error multiple times, on gordon (SDSC) and
> our group's local cluster, both with implicit and explicit solvent. The
> only time that a metadynamics run has been restarted correctly (that
> preserves the information from the initial run) was while using a single
> replica.
>
> On Thu, Mar 19, 2015 at 5:26 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> You shouldn't have to enable keepHills to continue a simulation. Have
>> you tried to reproduce the error, i.e. have you tried to run jobs 1 and 2
>> consecutively? If they are too expensive to recalculate, try with a short
>> job of 10-20 ps to reproduce the problem.
>>
>> Giacomo
>>
>> On Thu, Mar 19, 2015 at 11:24 PM, Amy Rice <arice3_at_hawk.iit.edu> wrote:
>>
>>> Hi Giaocmo,
>>> My apologies for the delayed response. All of the replicas are accessing
>>> the same registry file, and the the registry itself is giving the correct
>>> path to the state and hills files for each replica. The state files are all
>>> up-to-date and have the expected step number for the end of the original
>>> simulation. I noticed that the registry is also pointing to ".hills" files
>>> for each replica; however, I didnt use the "keepHills" option so these
>>> files are all empty. Is it possible this is the source of the problem?
>>> Thank you,
>>> - Amy
>>>
>>> On Sun, Mar 15, 2015 at 10:47 AM, Giacomo Fiorin <
>>> giacomo.fiorin_at_gmail.com> wrote:
>>>
>>>> Sorry for the incomplete email. The keyword replicasRegistry indicates
>>>> the path to a text file where the latest version of the state file for each
>>>> replica can be found.
>>>>
>>>> Can you check if all replicas see the same registry file, and that the
>>>> contents of it are up-to-date with the final snapshot of your simulation?
>>>>
>>>> Giaocmo
>>>>
>>>> On Sun, Mar 15, 2015 at 4:45 PM, Giacomo Fiorin <
>>>> giacomo.fiorin_at_gmail.com> wrote:
>>>>
>>>>> Hello Amy, the replicas all share the same bias: from the point of
>>>>> view of each replica, there are 300 kcal/mol of biasing energy in 7.5 ns.
>>>>> You have not simulated any of those systems longer than 7.5 ns, so that is
>>>>> the time during which the bias was added.
>>>>>
>>>>> You can find the documentation for multiple-replicas metadynamics here:
>>>>>
>>>>> http://www.ks.uiuc.edu/Research/namd/2.10/ug/node58.html#SECTION000135240000000000000
>>>>>
>>>>> Note that this feature doesn't use yet the replica-exchange syntax
>>>>> that is also used in scripts in the lib/replicas folder. It uses temporary
>>>>> files that are exchanged at regular intervals, not too frequently and
>>>>> asynchronously.
>>>>>
>>>>>
>>>>> On Thu, Mar 12, 2015 at 11:26 PM, Amy Rice <arice3_at_hawk.iit.edu>
>>>>> wrote:
>>>>>
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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/
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>
>>
>>
>>
>> --
>> 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
>

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