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
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