Re: Query regarding colvar distanceZ

From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Tue Dec 27 2016 - 19:07:07 CST

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

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