Re: A namd2.8b1 bug ?

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue May 10 2011 - 21:02:49 CDT

Nice catch! I broke spherical and cylindrical boundary conditions. It's
fixed now for the 2.8b2 release. Thanks!

-Jim

On Wed, 27 Apr 2011, charlie wrote:

> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:06 CST