AMBER Archive (2009)

Subject: Re: AMBER: CHCl3 solvent box

From: David A. Case (
Date: Mon Jan 05 2009 - 07:48:44 CST

On Mon, Jan 05, 2009, WJ Ding wrote:

> I built a solvent box of chloroform with tleap. When I visualized the pdb file
> with VMD, it is found that the bond lengths of C-Cl even in the same molecule
> are different (1.72-1.83 angstrom, I just cheked three molecules), which will
> cause the C-Cl bond to be cleaved during the MD calculation. I do not think tt
> is reasonable. Is there anyone who ever encountered this problem? What's
> wrong with my solvent box?

Bonds can never be cleaved in MD simulations -- why not minimize or run
dynamics and see what happens.

You didn't say how to created the solvent box, but my guess is that you
used the CHCL3BOX unit. This file indeed has unequal C-Cl bond lengths
-- it could be a snapshot from an MD simulation, although the magnitude
of the deviations from ideality seems large.


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