Subject: Re: CCL:Rigid body simulations in charmm

From: Konrad Hinsen <hinsen/at/cnrs-orleans.fr>
Date: Tue, 4 May 2004 12:01:37 +0200

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?
>
Standard SHAKE is not suited for rigid bodies exceeding four atoms. 
There is an extension for those cases, but it doesn't seem to be very 
popular. There are also many other algorithms for simulating rigid 
molecules. However, I don't know if any of them are available in 
CHARMM.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire Lion Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: hinsen/at/llb.saclay.cea.fr
---------------------------------------------------------------------

---

From: Richard Gillilan <reg8)at(cornell.edu>
Date: Tue, 4 May 2004 11:20:40 -0400

> codes are available anywhere yet.  The older program DPOLY
> can do this kind of simulation.

Sorry for my poor choice of words here (the program is
actively maintained and fairly recent) and the
typo, the program is called DL_POLY and can be found
at http://www.cse.clrc.ac.uk/msi/software/DL_POLY/.
Looks like it has been used for liquid simulations too.

Richard Gillilan
MacCHESS, Cornell