Subject: Re: CCL:Rigid body simulations in charmm

From: Rick Venable <rvenable..at..pollux.cber.nih.gov>
Date: Mon, 3 May 2004 12:28:14 -0400

On Mon, 3 May 2004, Ravindra VenKatramani wrote:
>            I have a small (18 atom) dipeptide in DMSO solution. I
> would like to perform a simulation keeping both the peptide and the
> solvent rigid.
>       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?

If there are freely rotatable single bonds, constraining the bond
lengths isn't sufficient.  Also, as the potential is a balance of all
the terms, turning off the ANGLE and DIHEDRAL terms can lead to
distortion of the structure away from accepted geometries.  A couple
alternatives for the mini-peptide are:

[1] CONS HARM BESTFIT (cons.doc); the peptide can essentially be RMS
restrained vs. its initial geometry, w/o restricting translation or
whole molecule rotation.  The atom selection used will determine how
much of the molecule is restrained.

[2] CONS IC (cons.doc, intcor.doc); the bonds, angles, and dihedrals can
be restrained vs. their initial geometry.  An edited IC table may be
desirable, to allow free rotation of e.g. methyl groups while
restraining the backbone and main sidechain configurations.

The RESIDUE description for DMSO should probably have dummy C-C and O-O
bonds with zero force constant, so that SHAKE can be used to make the
molecule rigid, as is done for the TIP3 model via the dummy H-H bond.

Finally, be sure to minimize using the exact same setup (SHAKE, boundary
conditions, non-bond options) as will be used for the simulation.

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable..at..nih.gov
ALT email:  rvenable..at..speakeasy.org
-------------------------------------
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                         Homer
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From: Richard Gillilan <reg8*at*cornell.edu>
Date: Mon, 3 May 2004 15:50:22 -0400

On Monday, May 3, 2004, at 01:02 AM, Ravindra VenKatramani wrote:

>
> Dear Group,
>
>            I have a small (18 atom) dipeptide in DMSO solution. I would
> like to perform a simulation keeping both the peptide and the solvent
> rigid.
> 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?
>
> Regards
> Ravi

Yes, there are several alternative ways which are more efficient and
numerically stable. I remember reading somewhere that SHAKE is
problematic when trying to define true rigid bodies. There is a
program called MBO(N)D available from Accelrys (I don't know if
there is a free version or not, but the code is related to CHARMM
I think ... I have no relationship to this program or
the company and have no experience running it). I believe the
program was described in J. Comput. Chem. a few years ago:
Chun HM et. al. J. Comput. Chem. 2000, 21, 159

There have also been many articles on direct rigid body integration
(most recently by Miller et. al. JCP 2002, 116, 8649 ...
see also Dullweber, JCP 1997, 107, 5840). Don't know if their
codes are available anywhere yet.  The older program DPOLY
can do this kind of simulation. XPLOR also implements it, though the
algorithm they use is rather old now. You may find some other codes
that are specialized for liquid simulation ... I would love to know 
about
them.

  Richard Gillilan
  MacCHESS, Cornell