From: wang (c00jsw00_at_nchc.org.tw)
Date: Wed Mar 25 2009 - 00:57:33 CDT
Dear all ,
I succeed to compile the cuda version of NAMD 2.7 b1.
When I ran a case, the program stopped in the minimize step 553.
And there is any error message occurred .
Could you tell me how to fix the problem ?
Thank you .
Y. T Wang
input file
----------------------------------------------------------------------------------------------------------------------------------------
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure cg27wang.psf
coordinates cg27wang.pdb
set temperature 310
set outputname cg
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters rbcg-2007.par
temperature $temperature
# Force-Field Parameters
exclude 1-2
cutoff 12.0
switching on
switchdist 9.0
pairlistdist 16.0
hgroupcutoff 0
# Integrator Parameters
timestep 5.0
nonbondedFreq 1
stepspercycle 20
# Constant Temperature Control
langevin off
langevinPiston off
# Periodic Boundary Conditions
cellBasisVector1 150.0 0. 0.
cellBasisVector2 0. 150.0 0.
cellBasisVector3 0. 0 150.0
cellOrigin 0.0 0.0 0.0
wrapAll on
margin 6.0
dielectric 20
# Output
outputName $outputname
restartfreq 10
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels $temperature
run 20000000
output
---------------------------------------------------------------------------------------------------------------------------------------------
PRESSURE: 553 4.1798e+06 -231322 120605 -231322 4.15516e+06 -222828
120605 -222828 4.16118e+06
GPRESSURE: 553 4.1798e+06 -231322 120605 -231322 4.15516e+06 -222828
120605 -222828 4.16118e+06
ENERGY: 553 235.3469 746.7691 1723.1719 0.0000 0.0000 47938516.6039
0.0000 0.0000 0.0000
47941221.8918 0.0000 47941221.8918 47941221.8918 0.0000 4165380.2214
4165380.2214 3375000.0000 4165380.2214 4165380.2214
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