Re: [AMBER] Disappearing common atoms in Amber 10 with TI

From: Khavrutskii, Ilja <>
Date: Mon, 20 Jul 2009 12:46:38 +0100

What is the reason that makes removing X-H bond constraints so desirable for TI calculations?
Also, I would like to use soft cores, but I was under the impression that you do not have any of the soft Coulomb potentials implemented. This makes the vdW soft core potential less useful for me. Please let me know if you actually have the soft Coulomb implemented but undocumented, and how to use it.

On 7/17/09 7:41 AM, "case" <> wrote:

On Thu, Jul 16, 2009, Khavrutskii, Ilja wrote:

> What would be the best way to ensure that vc-vh bonds are SHAKEn?

I think you want the opposite: use the noshakemask to ensure that the
corresponding real c-h bonds are *not* shaken.

I really recommend using softcores instead for this sort of thing. First, as
you have found, you have to be very careful in setting up dummy atoms, and you
do have to make sure that everything is completely compatible between the two
endpoints. Amber doesn't check for everything that could go wrong. Plus, as
Thomas as pointed out, getting good convergence without the softcore option is
a tricky business in itself.


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