From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Tue Dec 27 2016 - 20:47:16 CST
Thanks a lot Joshua and Giacomo
I think the large jump in velocity was coming from distanceZ trying to flip
the position of the two atoms, I swapped the atomnumbers in input file and
it is working now.
On Wed, Dec 28, 2016 at 12:07 PM, Peter Mawanga <
peter.mawanga.lagos_at_gmail.com> wrote:
> Thanks a lot!
>
> I think *distance* is a scalar colvar and *distanceZ* a vector one. The
> starting value is negative, it should be the reason behind it not working I
> presume?
>
> # step polymerbeadseparation
> 0 -3.00000000000000e+01
>
> On Wed, Dec 28, 2016 at 6:20 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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.m
>>>> awanga.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 <(215)%20204-4213>
>>
>> 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
>>
>>
>>
>
>
> --
> Cheers
> Peter
>
-- Cheers Peter
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