From: Revthi Sanker (revthi.sanker1990_at_gmail.com)
Date: Thu Jul 25 2013 - 02:40:42 CDT
Dear Sir,
Thank you so much for the suggestions. the steps are doing fine. And i do
not have any particular reason for vacuum minimisation and so will proceed
to solvation directly.
thank you once again.
Revathi.S
M.S. Research Scholar
Indian Institute Of Technology, Madras
India
_________________________________
On Wed, Jul 24, 2013 at 7:08 PM, Niklaus Johner <niki.johner_at_gmail.com>wrote:
> 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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