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?
> >>

---

From: Ravindra VenKatramani <ardnivar|at|pas.rochester.edu>
Date: Tue, 4 May 2004 15:15:37 -0400 (EDT)

Yes, This was also suggested by Rick Venable in response to my mail and i
think it`s the best way to proceed. I now define all the bonds for my dipeptide
and then use IC GENERATE, IC FILL (I have the cartesian coords) and CONS
IC BONDS ANGLES DIHED IMPR to hold the peptide fixed.
         It seems that i do not need to specify the IC`s by hand as
charmm can generate them from the bond information. One question is what
is the upper limit on the force constant values? it should depend on the
timestep right?

Regards
Ravi

On Tue, 4 May 2004, Jerome Baudry wrote:

> jerome|at|scs.uiuc.edu
> > [mailto:chemistry-request|at|ccl.net]On
> > Behalf Of Konrad Hinsen
> > Cc: chemistry|at|ccl.net

---

From: hinsen{at}cnrs-orleans.fr
Date: Tue, 4 May 2004 23:50:27 +0200

> IC command, but doable since you're dealing with a dipeptide..

If I understand correctly what this command does, it adds a restraint  
force. This is *not* equivalent to fixing a coordinate. There is an  
important technical difference (a high force constant requires a very  
short integration time step, whereas a fixed internal coordinate  
permits a larger one), and also a difference in thermodynamic averages.  
The limit of a restraint force when the force constant goes to infinity  
is not a fixed coordinate.

Depending on the application, this point may not be important, but one  
should be aware of it.
--
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Konrad Hinsen
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Fax: +33-1 69 08 82 61
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