Subject: RE: Rigid body simulations in charmm

From: "Jerome Baudry" <jerome~at~scs.uiuc.edu>
Date: Tue, 4 May 2004 11:07:33 -0500

What about fixing all internal coordinates in the to-be-rigid-molecule:
using the CONS ICcommand ?
all bonds must have the same restraint constant (same for angles, dihedrals
etc..) , but since you want to define a rigid body, you can use one unique
very high constant. You would have to define explicitly all ICs in the CONS
IC command, but doable since you're dealing with a dipeptide..

----------------------------------------------------------
Jerome Baudry, Ph.D.       Senior Research Scientist, VizLab Manager.
School of Chemical Sciences    University of Illinois at Urbana-Champaign
505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801
 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120;    e-mail:
jerome~at~scs.uiuc.edu

> -----Original Message-----
> From: Computational Chemistry List
> [mailto:chemistry-request~at~ccl.net]On
> Behalf Of Konrad Hinsen
> Sent: Tuesday, May 04, 2004 5:02 AM
> To: Ravindra VenKatramani
> Cc: chemistry~at~ccl.net
> Subject: CCL:Rigid body simulations in charmm
>
>
> On May 3, 2004, at 7:02, Ravindra VenKatramani wrote:
>
> >       My first thought is to define the dipeptide structure only
> > thorugh
> > bonds (no angles or dihederals) and use SHAKE to keep the peptide
> > fixed.
> > Doing so i`m running into SHAKE convergence problems during
> the heating
> > and equilibration stage. Am i missing something in this
> simple minded
> > approach? Is there an alternate way to perform rigid body
> simulations?
> >>