Re: Equilibration

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Jul 19 2011 - 14:42:06 CDT

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:13 CST