From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Sep 02 2010 - 16:42:56 CDT
jane,
NBFIX terms are lennard jones parameters between
pairs of atoms that are not derived from the mixing
rules. i.e. they override the mixing rule parameters.
i think the GPU code doesn't currently support those
but rather stores the per atom type parameters in some
fast memory area and does the mixing on the fly.
i suppose that this is true for amber as well, even though
those may be called differently or always computed or
stored explicitly. CHARMM parameter files have those
terms listed (e.g. for different metal ions) in a section
called NBFIX (hence the error message).
cheers,
axel.
On Thu, Sep 2, 2010 at 4:45 PM, Jane Ren <j2ren_at_ucsd.edu> wrote:
> Hi Felipe,
>
> Thanks for your reply.
> Could you tell me how the NBFIX terms are identified in the NAMD paramter files? My parameter file below does not have any parameters with the NBFIX prefix.
>
> Thank you.
> ________________________________________
> From: felmerino_at_uchile.cl [felmerino_at_uchile.cl]
> Sent: Wednesday, September 01, 2010 8:54 PM
> To: Jane Ren; namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: NAMD Cuda NBFIX Terms
>
> Hey,
>
> 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
>
> best
>
> felipe
>
> ----Mensaje original----
> De: j2ren_at_ucsd.edu
> Fecha: 01-09-2010 21:21
> Para: "namd-l_at_ks.uiuc.edu"<namd-l_at_ks.uiuc.edu>
> Asunto: namd-l: NAMD Cuda NBFIX Terms
>
> Hi,
>
> 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
>
> #PBC
> #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.
>
>
>
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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