Proteine-membrane simulation.

From: Yoav Beck (ucbpybe_at_ucl.ac.uk)
Date: Tue Aug 04 2009 - 10:08:55 CDT

Dear all,
I am trying to run membrane protein simulations, but can't minimize
successfully. I did combine the protein with the membrane, add water and
counter ions. Here is an extract of the outcome

PRESSURE: 0 9.46948e+15 -1.39942e+14 1.54387e+14 -1.39942e+14
1.11476e+16 -2.23902e+14 1.54387e+14 -2.23902e+14 1.02628e+16
GPRESSURE: 0 9.46948e+15 -1.39942e+14 1.54387e+14 -1.39942e+14
1.11476e+16 -2.23902e+14 1.54387e+14 -2.23902e+14 1.02628e+16
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 0 6937.4145 8879.2601 8448.2516
68.9126 -2395.3259 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 102300.0000 9999999999.9999 9999999999.9999

OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 1 6.02846e+14 4.11297e+12 -2.47166e+14 4.11297e+12 5.42603e+14
-5.55522e+13 -2.47166e+14 -5.55522e+13 5.3318e+14
GPRESSURE: 1 6.02846e+14 4.11296e+12 -2.47166e+14 4.11298e+12
5.42602e+14 -5.55522e+13 -2.47166e+14 -5.55521e+13 5.3318e+14
ENERGY: 1 150887.6550 46650.6159 9886.1746
961.3403 -11626.6565 9999999999.9999 0.0000
0.0000 0.0000 9999999999.9999 0.0000
9999999999.9999 9999999999.9999 0.0000 9999999999.9999
9999999999.9999 102300.0000 9999999999.9999 9999999999.9999
..
MINIMIZER SLOWLY MOVING ATOMS WITH BAD CONTACTS DOWNHILL
PRESSURE: 97414 3.37775e+09 1.09931e+07 -2.91043e+06 1.09931e+07
3.40785e+09 -4.73679e+06 -2.91043e+06 -4.73679e+06 3.33555e+09
GPRESSURE: 97414 3.46918e+09 1.42519e+07 -3.95821e+06 1.4462e+07
3.44516e+09 -5.05362e+06 8.23537e+06 -6.33855e+06 3.44226e+09
ENERGY: 97414 4874838.3038 937325.7014 31077.7472
38194.6180 -69456.1542 1238003572.7904 0.0000
0.0000 0.0000 1243815553.0065 0.0000
1243815553.0065 1243815553.0065 0.0000 3373713815.5463
3452199270.2683 102300.0000 3373713815.5463 3452199270.2683
The high vdw number is probably due to clashes between atoms, but the
PRESSURE and GPRESSURE lines are ununderstandable to me. The script
looks like

set temperature 310
firsttimestep 0

exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

cellBasisVector1 66 0. 0.
cellBasisVector2 0. 31 0.
cellBasisVector3 0. 0. 50
cellOrigin 0. 0. 0.
wrapAll on
PME yes
PMEGridSizeX 72
PMEGridSizeY 32
PMEGridSizeZ 64

useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell yes
useConstantArea yes

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 100
xstFreq 250
outputEnergies 100
outputPressure 100

minimize 100000
reinitvels $temperature

Any help will be greatly appreciate.

Cheers,

Yoav.

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