From: Karol Kaszuba (karol.kaszuba_at_uwm.edu.pl)
Date: Tue Jan 16 2007 - 05:49:34 CST
Dear NAMD users,
I have a problem with restarting the simulation. I read all messages about it
in NAMD mailing list but I didn't find a solution.
1. I initailly minimized my complex and run MD (50000 steps = 100ps) with
totally fixed protein.
2. I want to restart a simulation but without initiall energy minimization. At
the beginning of the run I obtained an error (see a message attached below)
which informs that I have some bad water - protein contacts - generally it is
possible but:
this same error - (realted to THESE SAME atoms) I obtained when I tried to run
my first equilibration phase (point 1) without E.min. It seems that NAMD
ignores previously generated: restart coordinates, velocities and cell
parameters and takes "standard" psf and pdb as the inputs.
I have been trying a various combinations of configure file (see a conf. file
below the error message)- still nothing.
Any help will be appreciable.
Yours sincerely,
Karol
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.3715e-16 AT 0.03125
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.00929e-16 AT 0.231756
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.70577e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.80873e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 2.91168e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 6.16001e-17 AT 11.9974
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.98523e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 8.0593e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
Info: Entering startup phase 8 with 22320 kB of memory in use.
Info: Finished startup with 25908 kB of memory in use.
TCL: Running for 100000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 1620!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
RESTART CONFIGURATION FILE:
structure structureX_wb_ion.psf
coordinates structureX_wb_ion.pdb
set temperature 310
set outputname structureX_wb_ion_all_system_moves
outputname $outputname
# Continuing a job from the restart files
if {1} {
set inputname structureX_fixed.restart
binCoordinates $inputname.coor
binVelocities $inputname.vel
extendedSystem $inputname.xsc
}
firsttimestep 0
# Input
paraTypeCharmm on
parameters par_all22_prot.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen no
wrapWater on
wrapAll on
#PME
PME yes
PMEGridSizeX 80
PMEGridSizeY 84
PMEGridSizeZ 84
# Constant Pressure Control
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
margin 2.5
restartfreq 10000 ;# 10000steps = every 20ps
dcdfreq 250 ;# = 400 x dcd
xstFreq 250
outputEnergies 100
outputPressure 100
# Fixed Atoms Constraint (set PDB beta-column to 1)
fixedAtoms on
fixedAtomsFile structureX_cys94-cys144_fixed.pdb
fixedAtomsCol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
run 100000 ;# 200ps
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