Re: problem restarting multiple walker metadynamics

From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Mon Mar 30 2015 - 13:23:24 CDT

Hi Giacomo,
I am using NAMD 2.9 and version 2012-03-23 of the colvars module. Thanks!

On Sat, Mar 28, 2015 at 5:50 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Hello Amy, before suggesting a solution I'd need the version of NAMD and
> the version of the colvars module you were using.
>
> There have been several changes recently, both in the colvars module and
> in how files are read and written by NAMD, which affect dramatically the
> best solution to your problem.
>
> Can you please email the version numbers? Thanks!
>
>
> Giacomo
>
>
> On Fri, Mar 27, 2015 at 12:48 PM, Amy Rice <arice3_at_hawk.iit.edu> wrote:
>
>> Thank you, I appreciate the help. In the meantime, is there any sort of
>> work around that you are aware of? I've been considering trying to somehow
>> combine the information from all of my .state files and restart the run
>> from this (changing the colvar to the proper value for each replica), but
>> I'm afraid this might affect the results obtained.
>>
>> On Thu, Mar 19, 2015 at 6:39 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
>> > wrote:
>>
>>> 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
>>>>
>>>
>>
>>
>> --
>> 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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