Re: Equilibration

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Thu Jul 21 2011 - 20:44:38 CDT

Chris gives good advice. However, it looks like Andres was indeed using
periodic boundaries, just spherical ones.

Perhaps the issue is merely one of visualization? In other words, if you
really are using PBC, then if your protein wanders off to the edge of the MD
cell, it doesn't matter in terms of the dynamics, because in fact the
protein is still surrounded by solvent; it might just "look funny" if you
visualize the coordinates without taking the PBC into account.

-Erik

-- 
C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania
On Tue, Jul 19, 2011 at 3:42 PM, Chris Harrison <charris5_at_gmail.com> wrote:
> Don't use a sphere, use a box with periodic boundary conditions.
> Otherwise, your only option is some form of non-physical restraint via
> colvars, fixedatoms, tclForces, or the restraints option in namd.
>
> -Chris
>
>
> On Tue, Jul 19, 2011 at 1:39 PM, Andres Morales N
> <andresmoralesn2_at_hotmail.com> wrote:
> >
> >  Dear NAMD Users:
> >
> > I am working with a cationic amphiphilic peptide named Bactenecin whose
> > linear sequence is RLCRIVVIRVCR. I worked with the peptide in a water
> > sphere. There was no problems in minimization and warming the system, but
> > during the equilibration the peptide tends to go outside the water
> sphere.
> > I believe it is not normal. Does anybody know how to avoid it?
> > The script I used for the euilibritaion was:
> >
> > structure          ../Estructuras/bact.psf
> > coordinates        ../Estructuras/bact.pdb
> > bincoordinates     ../Calentamiento300/bact_cal300.coor
> > binvelocities      ../Calentamiento300/bact_cal300.vel
> > set outputname     bact_eq
> > firsttimestep      0
> > paraTypeCharmm     on
> > parameters          ../Estructuras/par_all22_prot.inp
> > exclude             scaled1-4
> > 1-4scaling          1.0
> > cutoff              12.
> > switching           on
> > switchdist          8.
> > pairlistdist        13.5
> > margin    0
> > # Integrator Parameters
> > timestep            1.0  ;# 1fs/step
> > rigidBonds          all  ;# needed for 1fs steps
> > nonbondedFreq       1
> > fullElectFrequency  2
> > stepspercycle       20
> > # Output
> > outputName          $outputname
> > dcdfreq             1000
> > outputEnergies      100
> > # Boundary conditions
> > extendedSystem      ../Calentamiento300/bact_cal300.xsc
> > wrapWater           on
> > # Spherical boundary conditions
> > sphericalBC         on
> > sphericalBCcenter   1.272152066230774 -0.23037071526050568
> > -0.2613491117954254
> > sphericalBCr1       23.563667210382658
> > sphericalBCk1       10
> > sphericalBCexp1     2
> > # Restrains
> > fixedAtoms          on
> > fixedAtomsCol       B
> > fixedAtomsForces   on
> > # Constant Temperature Control
> > langevin            on    ;# do langevin dynamics
> > langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
> > langevinTemp        300
> > langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
> > # Equilibración
> > run            2000000
> >
> >
> >
> >
> > I wait that someone can help me with this.
> >
> >
> >
> > Thanks for your help.
> >
> >
> >
> >
> >
> >
> >  Hernán Andrés Morales Navarrete
> >
> > Biophysics and Molecular Modeling Group
> > Physics Department
> > Escuela Politécnica Nacional, Quito - Ecuador
> > Ladrón de Guevara E11-253.
> > Casilla 17-01-1253
> > http://www.ciencias.epn.edu.ec/~biomod/
> >
> >
> >
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu                            Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
>
>

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