From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Apr 20 2006 - 21:47:40 CDT
Running each part independently won't fix anything. The holes appear
because your system is not at the appropriate density and you are not
using constant pressure. Just turn on the constant pressure control
(either Nose-Hoover Langevin Piston or Berendsen, look at the NAMD user's
guide and NAMD tutorial for more details in www.ks.uiuc.edu) for at least
100 ps or more. The size of your box will eventually shrink and the holes
will disappear once the right density is reached.
Marcos
On Sun, 21 Apr 2002, Sting wrote:
> Thanks snoze pa! I'll try it.
>
> --Sting
>
> =================================
>
> try to run each part seperately.
> 1. minimization.
> 2. equlib.
> 3. free md
> goodluck
>
>
> On 4/19/02, Sting <stg1979_at_emails.bjut.edu.cn> wrote:
> Dear All,
>
> I am using namd to study trihelices in the water box. Minimization and
500ps CA restrained dynamics were performed. I found a strange
phenomenon: sevral holes without water formed in the water box(even afer
adding the water layer to 15 angstrom),and with the rotating of the
trihelices,the holes seem moving accordingly. Still when performing
SMD,the water holes remain and adjust while going on. I wondered how to
explain it and how to tackle the problem. Could anyone offer some help?
Thanks.
>
> ==========
> #forcefield
> paratypecharmm on
> parameters par_all27_prot_lipid.inp
>
> #molecules
> structure solvated.psf
> coordinates solvated.pdb
>
> temperature 310
>
> #temp & pressure coupling
> langevin on
> langevinTemp 310
> langevinDamping 1
> useGroupPressure yes
> #output
> outputname mini_eq
> outputEnergies 10
> restartfreq 500
> DCDfreq 500
> binaryoutput no
> binaryrestart yes
> outputTiming 100
> wrapAll on
> wrapNearest off
> wrapWater on
>
> #integrator
> timestep 2
> nonbondedFreq 2
> fullElectFrequency 4
> stepspercycle 20
>
> #approximations
> rigidBonds all
> rigidTolerance 0.00000001
> cutoff 12
> switching on
> switchdist 10
> pairlistdist 14
> #margin 3
> exclude scaled1-4
> 1-4scaling 1.0 # 1.0 for Charmm, 0.833333 for Amber
> dielectric 1.0
> PME on
> cellBasisVector1 90.045 0 0
> cellBasisVector2 0 32.650 0
> cellBasisVector3 0 0 32.853
> cellOrigin 441.652 0.379 0.0423
>
> PMEGridSizeX 90
> PMEGridSizeY 32
> PMEGridSizeZ 32
>
> #
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile fix_ca.pdb
> fixedAtomsCol B
>
> #
> minimize 0
> #
> minimize 10000
> #
> run 250000
>
>
> Sting
>
> stg1979_at_emails.bjut.edu.cn
> 2006-04-20
>
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