AMBER Archive (2006)

Subject: RE: AMBER: ibelly not work

From: Andy Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Thu Dec 07 2006 - 06:33:24 CST

Dear Ross and JunJun,

I disagree with this statement about belly and constant pressure being
incompatible. I run this scheme during one of my equilibration phases
(system having been warmed up at constant volume), keeping the protein
fixed with belly and allowing my water molecules to move. I have never
had any errors reported from the constant pressure part of sander.

The set up works fine, as (I think) it is the position of the centers of
mass of the molecules that are scaled. So, my protein is a single fixed
entity in thousands of water molecules.

However, I'm not certain what the effect will be when restraining
individual atoms where the rest of the molecule is being scaled. In the
older versions of AMBER, where per atom scaling was allowed, I would
imagine you'd have more problems.

However, I do agree with Ross, that use of restraints is better for
fixing small parts of large systems.

Hope this is of some help.

Andy

On Wed, 2006-12-06 at 16:07 -0800, Ross Walker wrote:
> Dear JunJun,
>
> I do not believe that it is possible to use Belly with constant pressure. It is likely disabled because it corrupts the virial and so prevents the barostat from working. It is also extremely unphysical and it is not obvious why you would want to do it. The concept of pressure when you have some atoms artificially constained is not well defined.
>
> If you specifically want to keep part of your system fixed in a location then I think the best way to do this is to use restraints and set a reasonably high restraint force.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
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>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of JunJun Liu
> > Sent: Wednesday, December 06, 2006 15:23
> > To: amber_at_scripps.edu
> > Subject: AMBER: ibelly not work
> >
> > Dear all,
> > I'm using AMBER8. I want to fix some atoms during MD, then I use
> > ibelly=1. However I find those atoms cannot be fixed unless I change
> > "ntb=2 ntp=1" to "ntb=1, ntp=0".
> > Could you please give me some idea on how to fix atoms at
> > constant
> > pressure(ntb=2)?
> >
> > # Control section
> > &cntrl
> > nstlim=50000 , dt=0.002, ntx=1, irest=0, ntpr=500,
> > ntwr=500,ntwx=500 ,
> > tempi=10.0, temp0=298.15, dtemp=10.0, ntt=1, tautp=2.0, ig=2858,
> > ntb=1, ntp=0,
> > ntc=2, ntf=2,
> > nrespa=1,
> > cut = 10.0,
> > ibelly=1,
> > &end
> > &ewald
> > &end
> > G1
> > ATOM 1 1288
> > END
> > G2
> > ATOM 1290 1290
> > END
> > G3
> > ATOM 1302 1818
> > END
> > END
> >
> >
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>
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-- 
Cat, n.: Lapwarmer with built-in buzzer.
+----------------------------------------------------------------------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                    |
|      Phone 020 7631 6869 (Work) or 07763 490 360 (Mobile)            |
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