Re: AMBER: Topology file problem in TI !

From: Thomas Steinbrecher <>
Date: Wed, 7 Mar 2007 11:35:29 -0800 (PST)

Hi Ilyas,

> I could not understand what u meant by 'simulation instabilities' when a
> vdw/charge transformation is done together. I have a couple of systems

If you have a disappearing atom with a non-zero charge, then at high
lambdas another (non-disappearing) atom of opposite charge can come close
enough to it so that coulomb attraction can overcome what is left of vdw
repulsion making atoms 'fall into each other' and crashing your
simulation with extremely high forces.

The reason you do not see that happen might be that, from your
description, I guess you are disappearing hydrogens bound to bulky
hetero atoms like O. In this case, the hetero atom vdw repulsion prevents
other atoms in coming to close to the disappearing hydrogen for bad things
to happen. For the same reason, the HO-type hydrogen in parm99.dat can get
away with a zero-vdw size, because it is always bound to a OH-type oxygen.

I would predict that if you disappered bigger parts of molecules, say an
ethyl-chain, without first discharging them, you would run into trouble,
which is what I meant by simulation instabilities.



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 11 2007 - 06:07:10 PDT
Custom Search