From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 03 2004 - 10:32:58 CST
Hello Cetin,
There are some definite problems here. Do you see any errors when
creating the psf file or during solvation of the protein. Also, the
coordinates for your system box seem to be irregularly formated. No
commas are needed, just spaces.
Brian
> Hi,
>
> I am running a protein dynamics with namd using PB conditions, when checking
> the first equilibration trajectory , I observe water molecules at the edges
> leaving the box. Water molecules leaving the box something expected, but
> removal of a portion at whole is something weird I guess , although my protein
> moves the opposite side of the box.
>
> I am also having a coor file problem, vmd does not open it, but namd accepts
> same coor files as input. vmd says
>
> Inconsistent atom count in file 'lyz_300.coor'.
> ERROR) Could not read file lyz_300.coor
>
> I have used different molecules and combinations for test, even coor files
> produced after namd tutorials failed to open.
>
> Here below is my config file, also picture of my protein with strange? water
> movement is
> http://students.sabanciuniv.edu/~cetinb/namd/lys.jpg
>
> I will also be glad if you comment on this conf. file .
>
> Thanks for advance.
> Cetin Baloglu
>
> set TEMP 305
> coordinates lyz_305.coor
> structure lysozyme.psf
> paraTypeCharmm on
> parameters par_all27_prot_lipid.inp
> outputname lyz_305_eq
> binaryoutput no
> DCDfile lyz_305_eq.dcd
> DCDfreq 1000
> outputEnergies 1000
> outputMomenta 0
> outputPressure 0
> outputTiming 0
> numsteps 1
> timestep 2.0
> rigidBonds all
> useFlexibleCell no
> useConstantArea no
> LangevinPiston off
> stepspercycle 20
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 13.5
> cellBasisVector1 48.0, 0, 0
> cellBasisVector2 0 , 45.0, 0
> cellBasisVector3 0 , 0, 54.0
> cellOrigin 0.73 22.08 19.69
> wrapWater on
> PME on
> PMEGridSizeX 48
> PMEGridSizeY 45
> PMEGridSizeZ 55
> useGroupPressure yes
> exclude scaled1-4
> temperature $TEMP
> 1-4scaling 1.0
> seed 12345
> langevin off
> langevinHydrogen off
> rescaleFreq 10000
> rescaleTemp $TEMP
> run 250000
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
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