Re: [AMBER] Chloroform in Amber, a rigid model?

From: Jason Swails <>
Date: Fri, 30 Dec 2011 00:45:15 -0500

No, it's not rigid. The only reason that water is rigid, as I understand
it, is because H-heteroatom bonds vibrate at a very high frequency -- much
higher than most other oscillatory motions. Hence, by SHAKEing water
molecules, you can use a longer time step, improving the efficiency of your
simulation for that reason.

However, I don't expect this to be the case for chloroform, so why exactly
do you want to SHAKE it in the first place?

That said, based on the way sander is set up (haven't looked too much into
pmemd), unless you "trick" the prmtop into considering the chloroform Cl
atoms to be Hydrogen, it's actually rather difficult to _just_ SHAKE the
C-Cl bonds in the solvent but not any of the other heteroatom-heteroatom
bonds in the solute that you don't want to SHAKE.

Perhaps others can offer advice borne from more experience with this type
of simulation.


On Thu, Dec 29, 2011 at 6:29 PM, Robert Woodwhite <> wrote:

> Dear all,
> I know Amber does have force field parameters for chloroform as in
> frcmod.chcl3. But can anyone tell me if this is a rigid model or flexible
> one? That is do I need to use shake to fix all the bonds and angles, as we
> shake rigid water models like TIPnP or SPC/E?
> Thanks
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Dec 29 2011 - 22:00:02 PST
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