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.
-- 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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