Re: equilibrated the system

From: apw397_at_soton.ac.uk
Date: Tue Jan 11 2005 - 09:58:27 CST

Perhaps its just me, but isn't this example file setting a temperature of
310K and then equilibrating it to 10K ?!!

To answer Xiaoqing's query check out:
http://www.ks.uiuc.edu/Research/namd/current/ug/node27.html#SECTION00091200000000000000

You should just have to edit a pdb input file, putting two columns on the
end of each line to include relevant parameters.

Adrian

Quoting Xiaoqing Wang <kitty_wxq_at_yahoo.com.cn>:

> Hi all
>
> I have downloaded an example of an equilibration (or “restrained”)
> run
> input file(restrained_md_example.in) in web site
> http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm .
>
> #forcefield
> paratypecharmm on
> parameters par_all27_prot_lipid.inp
> #molecules
> structure ions_added.psf
> coordinates ions_added.pdb
> bincoordinates after_min.restart.coor
> #binvelocities a.restart.vel
> extendedSystem after_min.xsc
> temperature 310
> #reassignFreq 100
> #reassignTemp 25
> #reassignIncr 25
> #reassignHold 300
> #constraints
> constraints on
> consref protein_only.coor
> conskfile protein_cons.pdb
> conskcol X
> #temp & pressure coupling
> langevin on
> langevinTemp 10
> langevinDamping 1
> #useGroupPressure yes
> #useFlexibleCell no
> #LangevinPiston on
> #LangevinPistonTarget 1
> #LangevinPistonPeriod 200
> #LangevinPistonDecay 500
> #LangevinPistonTemp 10
> #output
> outputname restr_md
> outputEnergies 10
> restartfreq 500
> DCDfreq 500
> binaryoutput no
> binaryrestart yes
> outputTiming 100
> wrapAll on
> wrapNearest on
> #integrator
> timestep 1
> nonbondedFreq 1
> 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
> PME on
> #cellBasisVector1 114.39 0 0
> #cellBasisVector2 0 120.16 0
> #cellBasisVector3 0 0 141.96
> PMEGridSizeX 120
> PMEGridSizeY 120
> PMEGridSizeZ 120
> #minimize 1000
> run 250000
>
> My question is how to prepare consref and conskfile files if I want to
> restrain protein?
>
> Thanks!!!
> --
> Wuhan University
> Wuhan
> China
>
>

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