Re: Re: water hole

From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Thu Apr 20 2006 - 22:15:42 CDT

Thanks Marcos!
  I have run my job according your suggestion.I'll show my result soon.

         -Sting

>
>
>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
>>

= = = = = = = = = = = = = = = = = = = =
                        

        崑

 
                                 
        Sting
        stg1979_at_emails.bjut.edu.cn
          2006-04-21

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