Re: NAMD Cuda NBFIX Terms

Date: Wed Sep 01 2010 - 22:54:45 CDT


The NBFIX terms are used to include an extra energetic component for certain nonbonded interactions (it is often used in coarse grained model for example). The NBFIX terms are included in the parameters file. If your model includes this kind of non-bonded interactions then find out why before removing them



----Mensaje original----
Fecha: 01-09-2010 21:21
Para: ""<>
Asunto: namd-l: NAMD Cuda NBFIX Terms


I am trying to run the CUDA version, but getting this error
"Reason: FATAL ERROR: CUDA-accelerated NAMD does not support NBFIX terms in parameter file."

So I'd like to remove the NBFIX terms, but I'm not sure where my NBFIX terms are...
Below is my parameter file, and it does not appear to contain any NBFIX parameters.

#set inpname free_eq
set outname free_eq2
firsttimestep 3997000

# input
amber yes
parmfile A.prmtop
ambercoor A.moved_ions.inpcrd.1
readexclusions yes
BinCoordinates free_eq.restart.coor
BinVelocities free_eq.restart.vel
ExtendedSystem free_eq.restart.xsc

# force field parameters
exclude scaled1-4
1-4scaling 0.833333
cutoff 14
switching On
switchdist 12
pairlistdist 16
margin 1.0

rigidBonds all
rigidTolerance 0.0005

# integrator params
timestep 1.0
numsteps 1000
nonbondedFreq 2
PME yes
PMEGridSizeX 147
PMEGridSizeY 140
PMEGridSizeZ 200
FullElectFrequency 2
stepspercycle 20
langevin on # do langevin dynamics
#langevinFile tempfile.pdb
#langevinCol O
langevinTemp 310 # bath temperature
langevinDamping 5 # damping coefficient (gamma) of 5/ps
langevinHydrogen no # don't couple langevin bath to hydrogens
#temperature 310

# Pressure Control for NPT ensemble
useFlexibleCell no
langevinPiston on
langevinPistonTarget 1.01325 # in bar -> 1 atm
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 310

#cellBasisVector1 93.887 0.0 0.0
#cellBasisVector2 0.0 95.414 0.0
#cellBasisVector3 0.0 0.0 157.937
#cellOrigin -62.3142 32.1950 44.971
wrapWater on
wrapAll on
wrapNearest on
xstFile free_eq2.xst
xstFreq 10000

# output
outputname free_eq2
dcdfile free_eq2.dcd
restartname free_eq2.restart
restartfreq 1000
dcdfreq 1000
binaryoutput yes
outputEnergies 1000

Also, could the NBFIX terms be coming from a file like A.prmptop?

Thank you.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:29 CST