From: Wen Li (liw_at_wadsworth.org)
Date: Mon Feb 07 2005 - 12:15:41 CST
Dear Dr. Fowler,
Thanks for your help. It seems now that namd is running fine here. I am
wondering if the warnings in output file meant any problems:
......
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
WRITING COORDINATES TO DCD FILE AT STEP 1000
WRITING COORDINATES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 1000
FINISHED WRITING RESTART VELOCITIES
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 1000
WRITING COORDINATES TO OUTPUT FILE AT STEP 1000
CLOSING COORDINATE DCD FILE
WRITING VELOCITIES TO OUTPUT FILE AT STEP 1000
==========================================
WallClock: 4546.512207 CPUTime: 4546.512207 Memory: 166144 kB
End of program
Thanks,
Wen
On Mon, 7 Feb 2005, Philip Fowler wrote:
> At a quick glance I would replace "PMEGradSizeX" by "PMEGridSizeX" and the
> same for Y and Z and see if that works.
>
> --Phil Fowler
>
>
>
>
> > Dear All,
> >
> > This is my first time running namd, using AMBER topology file and AMBER
> > restart file on a system including an RNA-protein complex, ions and a box
> > of water.
> >
> > An error message came from running "namd2 test.conf > test_output":
> >
> > FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> >
> > I attach the file test.conf below, and hope you could help me, thanks!
> >
> > # NAMD CONFIGURATION FILE FOR an RNA-Protein complex
> > #input files using AMBER topology file (parmfile myAmberParam.top)
> > #and Amber restart file (ambercoor myAmberRestart.rst)
> >
> > PARATYPECHARMM off
> >
> > amber on
> > parmfile myAmberParam.top #Amber topology file
> > readexclusions off
> >
> > # this Amber restart file is for an RNA-Protein complex,
> > #and includes neutralizing ions and a box of water.
> >
> > ambercoor myAmberRestart.rst
> >
> > outputname test_nmad
> >
> > #Shake to the bond H-mother atom (ntc =2, ntf = 2)
> > rigidBonds all
> >
> > #tol = 0.0005
> > rigidTolerance 0.0005
> >
> > #nstlim = 1000
> > numsteps 1000
> >
> > # ntpr = 100
> > outputEnergies 100
> > ntwr = 100
> > restartfreq 100
> > DCDfreq 100
> >
> > #dt = 0.002
> > timestep 2
> >
> > temperature 30
> > cutoff 9
> > switching off
> >
> > PME on
> > cellBasisVector1 80.1563 0.0 0.0
> > cellBasisVector2 0.0 78.6237 0.0
> > cellBasisVector3 0.0 0.0 74.9825
> >
> > PMEGradSizeX 80
> > PMEGradSizeY 80
> > PMEGradSizeZ 80
> >
> >
> > Wen
>
> --
> Philip Fowler,
> PhD Student
> Centre for Computational Science,
> UCL Chemistry
>
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