Hi Jason
Thank you for the reply. I ask this because I found that all the published
force filed models for chloroform, either additive or polarizable, are
rigid model. That's the geometry is fixed during simulation, Only L-J and
electrostatic term is used for energy. Such as the one by W. Dietz, K.
Heinzinger and Dang et al.
And, I found that those parameters in Amber have very similar value to
those published rigid models.
So can you tell me where the parameters for chloroform in Amber comes
from? Is there any paper published for the parameter optimization and
liquid properties verification. I could not found any information about
that.
Thanks and happy new year!
2011/12/30 Jason Swails <jason.swails.gmail.com>
> 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.
>
> HTH,
> Jason
>
> On Thu, Dec 29, 2011 at 6:29 PM, Robert Woodwhite <robwowt.gmail.com>
> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 30 2011 - 10:00:03 PST
