Hi,
I am using internal dynamics in my annealing (IVM) protocol.
However,I still see in my output, the angle and bond terms are still
changing dramatically. According to the algorithm, these energies
should not change so much. In the test file in eginput/protG/
anneal.py.out, the energies does not drift so much.I am wondering
where the problem is and how the program works when they group atoms
together in torsion angle dynamics. I attached part of my output
below. I really appreciate it if you can take a look at it.
Besides, I keep seeing warnings like "Ran out of space.
RESIZING", any idea what is going on? Is it likely a problem?Any help
is greatly appreciated.
Lei
>
> **********************************************************************
> *****
> ********
>
> refine_solution2.py(302): protocol.initDynamics(dyn,
> refine_solution2.py(303): potList=potList, #
> potential terms to use
> refine_solution2.py(304): bathTemp=init_t,
> refine_solution2.py(305): initVelocities=1,
> refine_solution2.py(306):
> finalTime=200, #
> stops at 10ps or 5000 steps
> refine_solution2.py(307):
> numSteps=100000, #
> whichever comes first
> refine_solution2.py(308): printInterval=100)
> refine_solution2.py(305): initVelocities=1,
> refine_solution2.py(306):
> finalTime=200, #
> stops at 10ps or 5000 steps
> refine_solution2.py(307):
> numSteps=100000, #
> whichever comes first
> refine_solution2.py(308): printInterval=100)
> refine_solution2.py(310): dyn.setETolerance( init_t/100 )
> #used to
> det. stepsize. default: t/1000
> refine_solution2.py(311): dyn.run()
> AT_Build::buildNode: cycle link found between atoms 109 TYR 7 CD2
> and 106
> TYR 7 CG
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 360 PRO 22 CD
> and 351
> PRO 22 N
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 543 PHE 33 CD2
> and 540
> PHE 33 CG
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 596 PHE 36 CD2
> and 593
> PHE 36 CG
> removing bond.
> AT_Build::buildNode: cycle link found between atoms 702 PHE 42 CD2
> and 699
> PHE 42 CG
> removing bond.
> MAKINB: Ran out of space. RESIZING
> MAKINB: mode 3 found 0 exclusions, 0 interactions
> (1-4) and
> 0 GB exclusions
> MAKINB: Ran out of space. RESIZING
> MAKINB: mode 3 found 2921 exclusions, 0 interactions
> (1-4) and
> 2921 GB exclusions
> *--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t=
> 0.001 --*
> | E(kin)+E(poten)= 19289.551 E(kin)= 16482.983 temperature=
> 6090.025 |
> | E(poten)= 2806.5679990 grad= 13.5358613 ANGL=
> 13.5761242 |
> | BOND= 0.8928322 CDIH= 1178.7719619 IMPR=
> 0.3906830 |
> | RAMA= 0.3985943 VDW= 956.7098490 noe=
> 655.8279543 |
> *---------------------------------------------------------------------
> -----
> ----*
> *--- Dynamics ---- step= 100 ---- time= 0.054621 ----
> delta_t=0.00056459 --*
> | E(kin)+E(poten)= 30833.789 E(kin)= 15860.121 temperature=
> 5859.894 |
> | E(poten)= 14973.6671331 grad= 145.0876849 ANGL=
> 6570.7450174 |
> | BOND= 4887.3865428 CDIH= 922.8751677 IMPR=
> 1195.0822804 |
> | RAMA= 0.3730078 VDW= 790.2633561 noe=
> 606.9417608 |
> *---------------------------------------------------------------------
> -----
> ----*
> *--- Dynamics ---- step= 200 ---- time= 0.11042 ----
> delta_t=0.00054976 --*
> | E(kin)+E(poten)= 31318.550 E(kin)= 16217.945 temperature=
> 5992.101 |
> | E(poten)= 15100.6047748 grad= 145.1566581 ANGL=
> 6661.1279026 |
> | BOND= 4955.6012901 CDIH= 832.0514232 IMPR=
> 1203.7693866 |
> | RAMA= 0.3609247 VDW= 812.4356156 noe=
> 635.2582318 |
> **********************************************************************
> *************
