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.
-------
_________________________________________________________________
Spice up your IM conversations. New, colorful and animated emoticons. Get
chatting! http://server1.msn.co.in/SP05/emoticons/
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:36 CST