From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 19 2015 - 17:26:27 CDT
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/
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