RE: AMBER: regarding rigid molecules

From: Ross Walker <>
Date: Thu, 16 Oct 2008 07:53:29 -0700

I think what the original poster wants to do though is something akin to how
triangulated water works, I.e. not keep the CO2 fixed but keep it rigid and,
I assume, linear.

My first approach would be to shake the O-C-O bonds and see what happens
(using a shake mask that also shakes other H's if needed) although as Steven
points out this may not work for linear molecules. The other option would be
to shake the angle O-C-O as well as the bonds but sander's shake was never
designed to shake angles. You could specify an O-C-O angle parameter of 180o
with a very large force constant and O-C bonds with similarly high force
constants - this may cause integration problems due to high frequency
oscillations - but it may work, it would just need testing. You'd probably
need the fictitious O-O bond as well.

The main question though is why one wants rigid CO2 in the first place since
it won't help you with time step issues - unless you shake all the other
heavy atoms in your system.

All the best

> -----Original Message-----
> From: [] On Behalf
> Of Gustavo Seabra
> Sent: Thursday, October 16, 2008 6:35 AM
> To:
> Subject: Re: AMBER: regarding rigid molecules
> On Thu, Oct 16, 2008 at 5:34 AM, aneesh cna wrote:
> > Dear Amber Users,
> > I am using Amber 9.0 for simulating a system with 3-
> site
> > Carbon dioxide. I want to keep Carbon dioxide as rigid molecules
> through
> > out the simulation. How to do this in Amber? How to mention this in the
> > input file ?
> Just another option that wasn't mentioned yet... In principle (I
> haven't tried it) you could use the "belly" keyword. With it, you cen
> define a mask with the atoms you allow to *move*, in the "bellymask".
> So, for example if the CO2 is residue 1 on a parmtop file with 300
> residues, a bellymask like ":2-300" should do it. But again, I haven't
> tried it myself, so I'm not 100% sure it would work.
> Good luck,
> Gustavo.
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Received on Fri Oct 17 2008 - 05:11:07 PDT
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