Jump in Electrostatic Energy between two values

From: M. Madhu (madhu7_at_hotmail.com)
Date: Fri Feb 10 2006 - 14:33:17 CST

Dear All,

I am doing the tutorial - Gramicidin in explicit membrane (pope/water)
system - which is available at the following website:

http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on

I notice jumps in electrostatic energy between two values when I do the
equilibration (../../namd2 equil.namd).

The results are same either I use the original grama.psf, grama.pdb,
fix_backbone.pdb and restrain_ca.pdb or my own *.pdb and *psf files.
In both cases, I used the correct parameter (par_all27_prot_lipid.inp,
par-extraterms.inp) and topology (frotop_all27_prot_lipid.inp) files and
the same equil.namd file from the above website.

I tried different versions of namd (NAMD_2.5b1_Linux-i686,
NAMD_2.6b1_Linux-i686 and NAMD_2.6b1_Linux-i686-TCP)
on a linux machine, and also NAMD with Myrnet MX on MacOSX
(both serial and parallel). In all the cases, I observed the same probelm.

I will attach the equil.namd and a portion of the output file at the end of
this message for your reference.

Can someone explain why this is happening? Did anyone observe this
kind of behavior? Am I doing something wrong?

Thanks a lot.
Madhu
==================================================

------
equil.namd (original)
------

structure grama.psf
coordinates grama.pdb
temperature 0
parameters par_all27_prot_lipid.inp
parameters par-extraterms.inp
paraTypeCharmm on

outputEnergies 10
outputTiming 100
xstFreq 100
dcdFreq 100
wrapAll on
wrapNearest on

timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20

switching on
switchDist 8.5
cutoff 10
pairlistdist 11.5

cellBasisVector1 30.00 00.00 00.00
cellBasisVector2 15.00 25.98 00.00
cellBasisVector3 00.00 00.00 64.00
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 5

Pme on
PmeGridsizeX 32
PmeGridsizeY 32
PmeGridsizeZ 64

exclude scaled1-4
1-4scaling 1.0

fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol B

constraints on
consRef restrain_ca.pdb
consKFile restrain_ca.pdb
consKCol B

langevin on
langevinDamping 10
langevinTemp 310
langevinHydrogen no

langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310

useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate
independently
useConstantRatio yes # fix shape in x-y plane

binaryoutput off
outputname equil_out

# run one step to get into scripting mode
minimize 0

# turn off until later
langevinPiston off

# minimize nonbackbone atoms
minimize 1000
output min_fix

# min all atoms
fixedAtoms off
minimize 1000
output min_all

# heat with CAs restrained
# langevin on
run 3000
output heat

# equilibrate volume with CAs restrained
langevinPiston on
run 5000
output equil_ca

# equilibrate volume without restraints
constraintScaling 0
run 10000
===============================================

--------------
output file
--------------

Until 2000 step, electrostatic energy is pretty stable. After that it
jumps between two average values (initially) (~ -13500 and ! -72000).
Towards the end of the simulation, electrostatic energies were:

19990 (step no) -70034.7626 (elec)
20000 (step no) -11584.1788 (elec)

----
-------
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP  
          ELECT            VDW       BOUNDARY           MISC        KINETIC  
          TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG  
       PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
-----
ENERGY:    1995       418.2656       720.4155       526.1334         4.8189  
    -13486.2315       773.9508        14.4432         0.0000         0.0000  
    -11028.2039         0.0000    -11028.2039    -11028.2039         0.0000  
      -300.8747      -261.6859     49881.6000      -300.8747      -261.6859
BRACKET: 3.90647e-08 9.13854e-06 -5.59563 -5.43265 -5.28618
ENERGY:    1996       418.2656       720.4155       526.1334         4.8189  
    -13486.2314       773.9509        14.4432         0.0000         0.0000  
    -11028.2039         0.0000    -11028.2039    -11028.2039         0.0000  
      -300.8747      -261.6856     49881.6000      -300.8747      -261.6856
BRACKET: 2.24108e-08 1.40932e-05 -5.59563 -5.43265 -5.41802
ENERGY:    1997       418.2656       720.4155       526.1334         4.8189  
    -13486.2315       773.9509        14.4432         0.0000         0.0000  
    -11028.2039         0.0000    -11028.2039    -11028.2039         0.0000  
      -300.8747      -261.6856     49881.6000      -300.8747      -261.6856
BRACKET: 2.07454e-08 9.13854e-06 -5.59563 -5.43265 -5.43134
ENERGY:    1998       418.2656       720.4155       526.1334         4.8189  
    -13486.2315       773.9509        14.4432         0.0000         0.0000  
    -11028.2039         0.0000    -11028.2039    -11028.2039         0.0000  
      -300.8747      -261.6855     49881.6000      -300.8747      -261.6855
BRACKET: 1.85043e-10 1.4288e-06 -5.43265 -5.43274 -5.43134
NEW SEARCH DIRECTION
INITIAL STEP: 0.004096
GRADIENT TOLERANCE: 0.949101
ENERGY:    1999       417.6860       719.5507       526.0009         4.7204  
    -13487.2964       772.6279        14.5145         0.0000         0.0000  
    -11032.1961         0.0000    -11032.1961    -11032.1961         0.0000  
      -279.4100      -264.4487     49881.6000      -279.4100      -264.4487
TIMING: 2000  CPU: 199.964, 0.0937059/step  Wall: 205.708, 0.0953566/step, 0 
hours remaining, 0 kB of memory in use.
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP  
          ELECT            VDW       BOUNDARY           MISC        KINETIC  
          TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG  
       PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
ENERGY:    2000       417.6860       719.5507       526.0009         4.7204  
    -13487.2964       772.6279        14.5145         0.0000         0.0000  
    -11032.1961         0.0000    -11032.1961    -11032.1961         0.0000  
      -279.4100      -264.4487     49881.6000      -279.4100      -264.4487
WRITING COORDINATES TO DCD FILE AT STEP 2000
TCL: Writing to files with basename min_all.
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 2000
WRITING COORDINATES TO OUTPUT FILE AT STEP 2000
WRITING VELOCITIES TO OUTPUT FILE AT STEP 2000
TCL: Running for 3000 steps
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP  
          ELECT            VDW       BOUNDARY           MISC        KINETIC  
          TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG  
       PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG
ENERGY:    2000       417.6860       719.5507       526.0009         4.7204  
    -13487.2964       772.6279        14.5145         0.0000         0.0000  
    -11032.1961         0.0000    -11016.7962    -11074.5459         0.0000  
      -236.4965      -264.2065     49881.6000      -236.4965      -264.2065
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ENERGY:    2010       449.4838       714.3638       525.1769         5.4026  
    -72003.1496       780.0406        14.5464         0.0000       266.6365  
    -69247.4990        17.9442    -69236.6451    -69269.7547        10.8347  
        20.2634       -10.0813     49881.6000        -6.5605       -26.5967
ENERGY:    2020       471.1117       774.7314       524.6428         6.4140  
    -13509.7339       817.1226        14.4913         0.0000       465.3746  
    -10435.8454        31.3189    -10423.8931    -10453.5553        25.8458  
       265.8635       179.3526     49881.6000       187.4143       183.6712
ENERGY:    2030       489.2160       785.2061       527.0358         8.2814  
    -71995.7303       867.0948        14.5662         0.0000       611.0464  
    -68693.2836        41.1224    -68681.7813    -68704.0492        36.6506  
       798.2396       711.1190     49881.6000       634.4276       623.4282
ENERGY:    2040       503.1644       845.9927       532.9298         9.0437  
    -13466.3974       895.4291        14.6827         0.0000       714.3774  
     -9950.7777        48.0764     -9937.1276     -9960.9020        45.1187  
      1142.6115       940.9986     49881.6000       918.9373       902.8902
ENERGY:    2050       524.4092       862.7867       540.6675        10.1591  
    -71942.2701       910.4502        14.5249         0.0000       858.8665  
    -68220.4058        57.8002    -68206.5239    -68226.6751        53.9869  
      1542.6448      1367.3536     49881.6000      1255.8167      1259.8305
this pattern goes on till the end of the run.
-------
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