From: charlie (chengchangli123_at_163.com)
Date: Wed Apr 27 2011 - 02:23:56 CDT
Dear all:
When I minimize in namd2.8b1 , it will show:
"LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan
MINIMIZER RESTARTING CONJUGATE GRADIENT ALGORITHM
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan
... ... ... ... ..."
And when I run minimization in namd2.7, all is ok.
Is it a bug of namd2.8b1 ?
Best wishes O(กษ_กษ)O~
My configure file as follows:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ionized.psf
coordinates ionized.pdb
set temperature 310
set outputname gfp_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
parameters par_cro.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step #1
rigidBonds all ;# needed for 2fs steps #none
nonbondedFreq 1 ;#2
fullElectFrequency 2 ;#4
stepspercycle 10 ;#12
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 5000 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 9.53591537475586 70.61465454101563 -9.97712516784668
sphericalBCr1 42.0
sphericalBCk1 10
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels $temperature
run 100000 ;# 200ps
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