Tutorial-l Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Thu Mar 22 2012 - 09:27:33 CDT

Hello:
 I am following the membrane protein simulation protocol and I am trying
to equilibrium the system by following input file:

#############################################################
## JOB DESCRIPTION ##
#############################################################

# Min. and Eq. of protein
# embedded in POPC membrane, ions and water.
# Melting lipid tails. PME, Constant Volume.

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure ../step5_assembly.xplor.psf
coordinates ../step5_assembly.pdb
outputName popcwimineq-01

set temperature 310

# Continuing a job from the restart files
if {0} {
set inputname assembly
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc
}

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../toppar/par_all22_prot.prm;
parameters ../toppar/par_all27_na.prm;
parameters ../toppar/par_all36_carb.prm;
parameters ../toppar/par_all36_lipid.prm;
#parameters ../toppar/par_all36_cgenff.prm;
parameters ../toppar/par_all27_prot_lipidNBFIX.prm
#parameters ../toppar/toppar_water_ions.str;
#parameters ../toppar/toppar_all36_lipid_cholesterol.str;

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature

# Periodic Boundary conditions. Need this since for a start...
cellBasisVector1 76.6 0.0 0.0; # vector to the next image
cellBasisVector2 0.0 76.6 0.0;
cellBasisVector3 0.0 0.0 105.4;
cellOrigin 0.0 0.0 0.0; # the *center* of the cell

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)

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

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 80
PMEGridSizeY 80
PMEGridSizeZ 90
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 50
outputPressure 50

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile ../fix_prot.pdb
fixedAtomsCol B
fixedAtomsForces on
}

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
if {1} {
minimize 1000
reinitvels $temperature
}

run 500000 ;# 0.5 ns

But, it said:

LINE MINIMIZER BRACKET: DX 0 2.6857e-116 DU 0 0.000976562 DUDX -6.99825e+11
-6.99825e+11 -6.99328e+11
PRESSURE: 1000 2.44943e+08 -15852.3 -8789.58 -1.22401e+08 57042.6 13168.1
-7.04417e+07 10762.6 47620.3
GPRESSURE: 1000 2.44976e+08 -21451.9 10739 -1.22399e+08 56236.4 14020.2
-7.04015e+07 2695.95 69875.7
Warning: Energy evaluation is expensive, increase outputEnergies to improve
performance.
TIMING: 1000 CPU: 31.7652, 0.0319331/step Wall: 32.1639, 0.0321847/step,
0 hours remaining, 242.742188 MB of memory in use.
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG

ENERGY: 1000 39338.0170 79155.4220 10358.6830
296.6790 -145462.9569 -9999999999.9999 0.0000
0.0000 0.0000 -9999999999.9999 0.0000 -9999999999.9999
-9999999999.9999 0.0000 81682598.3462 81700597.5419
618440.8240 81682598.3462 81700597.5419

WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
OPENING COORDINATE DCD FILE
WRITING COORDINATES TO DCD FILE AT STEP 1000
WRITING COORDINATES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART COORDINATES
The last position output (seq=1000) takes 0.004 seconds, 242.945 MB of
memory in use
WRITING VELOCITIES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART VELOCITIES
The last velocity output (seq=1000) takes 0.001 seconds, 242.586 MB of
memory in use
REINITIALIZING VELOCITIES AT STEP 1000 TO 310 KELVIN.
TCL: Running for 500000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 15029!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 7201!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5436!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

WallClock: 57.276257 CPUTime: 55.389580 Memory: 243.140625 MB

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