From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Dec 27 2016 - 13:20:42 CST
Hello Peter, expandBoundaries is a convenience feature that is currently
being provided by the metadynamics bias only. If you are trying to use it
to push the boundary walls away as you go over them, that would defeat the
purpose of the walls.
Josh gave you very good suggestions, asking you twice to do a "run 0"
command. Since your initial configuration is unstable, please do that
first to see what is going on.
Giacomo
On Mon, Dec 26, 2016 at 12:39 PM, Peter Mawanga <
peter.mawanga.lagos_at_gmail.com> wrote:
> I tried with 10, 15, 20 as lower boundary; but it still is same. Anyway I
> had *expandboundaries* on to fix that. I presume I am missing something
> small but significant.
>
>
>
> On Tue, Dec 27, 2016 at 3:49 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> wrote:
>
>> Hmm… What happens if you ask for run 0? That will do an energy
>> evaluation, and should, if I remember correctly, also write the
>> colvars.traj just for that frame. Again, the only thing I can think of is
>> that the distance along the x axis is so small that distanceZ is hitting
>> the lower boundary potential and causing a mess. Others might have better
>> ideas.
>>
>> Josh Vermaas
>>
>> Director’s Postdoctoral Fellow
>> National Renewable Energy Laboratory
>> joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>
>>
>>
>>
>>
>> On Dec 26, 2016, at 8:17 AM, Peter Mawanga <peter.mawanga.lagos_at_gmail.com
>> <mailto:peter.mawanga.lagos_at_gmail.com>> wrote:
>>
>> colvars.traj output:
>>
>> # step polymerbeadseparation
>> 0 3.00000000000000e+01
>> 10000 2.91237590280440e+01
>> 20000 3.00346690073403e+01
>> 30000 2.82243021688464e+01
>>
>> I couldn't figure out why is this occurring, given both have the same
>> input files and are running on NAMD 2.12.
>>
>> Thanks
>> [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif]Peter
>>
>> On Tue, Dec 27, 2016 at 2:07 AM, Peter Mawanga <
>> peter.mawanga.lagos_at_gmail.com<mailto:peter.mawanga.lagos_at_gmail.com>>
>> wrote:
>> Hello Joshua
>>
>> The load balancing doesn't start for distanceZ case, hence I am not
>> getting any colvars.traj output either. This is the error:
>>
>> PRESSURE: 0 -2045.01 -9.4077 22.7297 -9.4077 -29.1219 -2.91884 22.7297
>> -2.91884 1.2482
>> GPRESSURE: 0 -2045.01 -9.4077 22.7297 -9.4077 -29.1219 -2.91884 22.7297
>> -2.91884 1.2482
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY MISC
>> KINETIC TOTAL TEMP POTENTIAL TOTAL3
>> TEMPAVG PRESSURE GPRESSURE VOLUME
>> PRESSAVG GPRESSAVG
>>
>> ENERGY: 0 7.0528 11.4618 0.0000
>> 0.0000 -75.4197 -155137.7401 0.0000 0.0000
>> 23072.9575 -132121.6877 309.2266 -155194.6452
>> -131515.7116 309.2266 -690.9601 -690.9601
>> 3468098.5652 -690.9601 -690.9601
>>
>> OPENING EXTENDED SYSTEM TRAJECTORY FILE
>> ERROR: Atom 2684 velocity is -312318 -220584 242621 (limit is 1200, atom
>> 11 of 43 on patch 345 pe 8)
>> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
>> patch 345 pe 8).
>> ERROR: Atom 51 velocity is 311893 220572 -242609 (limit is 1200, atom 7
>> of 43 on patch 355 pe 8)
>> ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
>> patch 355 pe 8).
>> ERROR: Exiting prematurely; see error messages above.
>>
>> Whereas for the case of distance colvar:
>>
>> PRESSURE: 0 -12.0398 -9.41329 22.7792 -9.41329 -29.1219 -2.91884 22.7792
>> -2.91884 1.2482
>> GPRESSURE: 0 -12.0398 -9.41329 22.7792 -9.41329 -29.1219 -2.91884 22.7792
>> -2.91884 1.2482
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY MISC
>> KINETIC TOTAL TEMP POTENTIAL TOTAL3
>> TEMPAVG PRESSURE GPRESSURE VOLUME
>> PRESSAVG GPRESSAVG
>>
>> ENERGY: 0 7.0528 11.4618 0.0000
>> 0.0000 -75.4197 -155137.7401 0.0000 0.0000
>> 23072.9575 -132121.6877 309.2266 -155194.6452
>> -132107.7606 309.2266 -13.3045 -13.3045
>> 3468098.5652 -13.3045 -13.3045
>>
>> OPENING EXTENDED SYSTEM TRAJECTORY FILE
>> LDB: ============= START OF LOAD BALANCING ============== 3.92203
>> LDB: ============== END OF LOAD BALANCING =============== 3.92287
>> Info: useSync: 0 useProxySync: 0
>> LDB: =============== DONE WITH MIGRATION ================ 3.96309
>> LDB: ============= START OF LOAD BALANCING ============== 5.12916
>> LDB: Largest compute 547 load 0.001950 is 0.2% of average load 0.822949
>> LDB: Average compute 0.000365 is 0.0% of average load 0.822949
>> LDB: Partitioning computes with target load 0.082295
>> LDB: Increased migratable compute count from 11400 to 11400
>> LDB: Largest unpartitionable compute is 0.001106
>> LDB: ============== END OF LOAD BALANCING =============== 5.1428
>> .
>> .
>> .
>>
>> colvars.traj output:
>>
>> # step polymerbeadseparation
>> 0 3.00000000000000e+01
>> 10000 2.91237590280440e+01
>> .
>> .
>> .
>>
>>
>> I couldn't figure out why is this occurring, given both have the same
>> input files and are running on NAMD 2.12.
>>
>> Thanks
>> Peter
>>
>> On Tue, Dec 27, 2016 at 1:12 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov
>> <mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
>> Hi Peter,
>>
>> What are the colvars values at time zero if you do it either way? It
>> should be reported in the (very short) colvars.traj file. It sounds like
>> what are reasonable boundaries and centers for the distance are not
>> reasonable for distanceZ, and so the simulation gets a gigantic force and
>> leads to atoms moving too fast.
>>
>> Josh Vermaas
>>
>> Director’s Postdoctoral Fellow
>> National Renewable Energy Laboratory
>> joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov><mailto:
>> joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>>
>>
>>
>>
>>
>>
>> On Dec 26, 2016, at 5:57 AM, Peter Mawanga <peter.mawanga.lagos_at_gmail.com
>> <mailto:peter.mawanga.lagos_at_gmail.com><mailto:peter.mawanga.
>> lagos_at_gmail.com<mailto:peter.mawanga.lagos_at_gmail.com>>> wrote:
>>
>> Hello everyone
>>
>> I want to apply colvar distanceZ for my NAMD ABF simulation instead of
>> distance. But each time the simulation keeps crashing (atoms moving too
>> fast) for distanceZ but works perfectly fine with distance colvar. Please
>> check the input file below:
>>
>>
>> colvarsTrajFrequency 10000
>> colvarsRestartFrequency 10000
>>
>> colvar {
>> name polymerbeadseparation
>> width 0.1
>> lowerboundary 5.0
>> upperboundary 30.0
>> lowerwallconstant 100.0
>> upperwallconstant 100.0
>> expandBoundaries on
>>
>> //distance
>>
>> distance {
>> group1 {
>> atomnumbers {17}
>> }
>> group2 {
>> atomnumbers {51}
>> }
>> oneSiteTotalForce yes
>> }
>>
>> //distanceZ
>>
>> distanceZ {
>> main {
>> atomnumbers {17}
>> }
>> ref {
>> atomnumbers {51}
>> }
>> axis (1, 0, 0)
>> oneSiteTotalForce yes
>> }
>>
>> abf {
>> colvars polymerbeadseparation
>> fullSamples 1000
>> hideJacobian yes
>> historyFreq 10000
>> }
>>
>> Please suggest some solution.
>>
>> Cheers
>> Peter
>>
>>
>>
>>
>>
>
>
> --
> Cheers
> Peter
>
-- Giacomo Fiorin Associate 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 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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