From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Dec 27 2016 - 19:14:06 CST
Yup, that would do it! Since your lower boundary is 5, and your are 35 away from it to start with, the force applied gets very big very quick (100*35^2=much much bigger than a typical bonded force). Switch the sign on your axis, and it ought to work as you expect.
-Josh
On 12/27/2016 06:08 PM, Peter Mawanga 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<mailto: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<mailto: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 <<mailto:Joshua.Vermaas_at_nrel.gov>Joshua.Vermaas_at_nrel.gov<mailto: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><mailto:<mailto:joshua.vermaas_at_nrel.gov>joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>>
On Dec 26, 2016, at 8:17 AM, Peter Mawanga <<mailto:peter.mawanga.lagos_at_gmail.com>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:
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<https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif%5DPeter>
On Tue, Dec 27, 2016 at 2:07 AM, Peter Mawanga <<mailto:peter.mawanga.lagos_at_gmail.com>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 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
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