From: Niklaus Johner (niki.johner_at_gmail.com)
Date: Wed Jul 24 2013 - 08:38:49 CDT
Hi,
Any particular reason you want to perform a vacuum minimization? If not, I would do the solvation and then start the equilibration process (i.e. minimization followed by constrained MD).
The solvation is done outside of namd, typically using psfgen in vmd. The restraints are put on your system in the namd inputfile, so you will typically have a first run with constraints and then restart (using the final positions and velocities of the first run) a run with no constraint. If you don't have a membrane in your system, the typical equilibration process is to restrain only the backbone of the protein and leave the waters free. Start with minimization and then several runs with decreasing constraint on the backbone (we use 1, 0.5 and 0.1). Then start the free MD. The restraints are added in the input file using:
# Harmonic constraint
# -------------------
constraints on # (off)
consref restraintfile.pdb
consexp 2
conskfile restraintfile.pdb
conskcol B
For the free MD you will simply remove those lines from your input file. I suggest you read the tutorials and manual.
Best,
N.
Niklaus Johner
Weill Cornell Medical College
Harel Weinstein Lab
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065
On Jul 24, 2013, at 3:37 AM, Revthi Sanker wrote:
> Dear all,
> I am a novice to performing simulations and NAMD. I intend to perform a vacuum minimization before solvating the protein. this is the script that I am using for this purpose. I was informed that we should restrain the the backbone atoms for this step. If so, how would I do that and how do I remove the restraints before proceeding to solvation? I would be grateful for help me in this regard.
>
> paraTypeCharmm on
> minimization on
>
> numsteps 2000
> structure ptn_psf.psf
> parameters modified_par_all36_prot.prm
> parameters par_all36_lipid.prm
> coordinates ptn_psf.pdb
> exclude scaled1-4
> 1-4scaling 1.0
>
> temperature 0
> seed 1234
>
> binaryoutput yes
> outputEnergies 1
> outputname ptn_gas_min
>
> switching on
> switchdist 8.5
> cutoff 10
> pairlistdist 12
>
> #periodic boundary conditions
> cellBasisVector1 144 0 0
> cellBasisVector2 0 144 0
> cellBasisVector3 0 0 144
>
> #PME
> PME on
> PMEGridSizeX 144
> PMEGridSizeY 144
> PMEGridSizeZ 144
>
> #IMD
> IMDon no
> IMDport 2030
> IMDFreq 1
>
> # position-restrained
> fixedAtoms on
> fixedAtomsFile fixed_atoms.pdb
> fixedAtomsCol B # 1.0 in this col.
> fixedAtomsForces on
>
> dcdfreq 250
> xstFreq 250
>
>
> thanks in advance :)
>
> Revathi.S
> M.S. Research Scholar
> Indian Institute Of Technology, Madras
> India
> _________________________________
>
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