Re: NAMD Cuda NBFIX Terms

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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