From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Mon Dec 26 2016 - 09:17:34 CST
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
Peter
On Tue, Dec 27, 2016 at 2:07 AM, Peter Mawanga <
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>
> 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>
>>
>>
>>
>>
>> On Dec 26, 2016, at 5:57 AM, Peter Mawanga <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
>>
>>
>
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