constraining water so that it does not get inside bilayer

From: Himanshu Khandelia (
Date: Mon Mar 06 2006 - 14:06:35 CST


During equilibration of a transmembrane peptide-bilayer system, I want to
avoid water entering the bilayer, mainly because I need the system to
equilibrate to the right area before running contraint-free dynamics. Is
there a way to setup planar harmonic constraints in NAMD ?

If not, I guess I will have set up constraints on all waters during
equilibration ?

If so, will the simulation crash if the area of the bilayer/peptide
assembly shrinks ?

Thanks a ton for the inputs !

Himanshu Khandelia

Doctoral Candidate,
Kaznessis Research,
Department of Chemical Engineering and Materials Science,
University of Minnesota

Mailing Address:

499, Walter Library,
117, Pleasant St. SE,
Minneapolis, MN 55455

Phone(o): 612-624-4945

On Sun, 5 Mar 2006, Himanshu Khandelia wrote:

> Hi,
> I was wondering if it was possible to have started a simulation in charmm,
> and continue it in NAMD ? I have already crossed equilibration and am into
> production while using charmm. Given that the force fields are the same,
> will this cause problems ? Importantly, will I be able to use the charmm
> restart file in NAMD ? If not, I will obviously have to restart the
> simulation run from scratch. Thank you very much for your inputs,
> -Himanshu

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