AMBER Archive (2005)Subject: Re: AMBER: Dummy Atom Types on both states
From: david.evans_at_ulsop.ac.uk
Date: Tue Feb 15 2005 - 11:29:39 CST
Hi,
Just a question to clarify this for myself:
Is this asymmetry because the equation (5) on page 133 of the Amber8
manual is asymmetric about
lambda = 0.5 when lambda > 1?
Gromacs, and probably other codes, use a 'soft core' potential, which
is apparently symmetric. So this could perhaps allow simulations with
dummy atoms at both end-points. But I haven't done any proper
experimenting. Is this related to what you (Thomas) are doing?
Thanks
Dave
--
David Evans
School of Pharmacy
University of London
---- Message from Thomas Steinbrecher <steinbrt_at_scripps.edu> at
2005-02-15 01:04:06 ------
>Hello
>
>> Dummy atoms are just atoms (or atom TYPES). They have some
parameters too,
>> except that the non-bonded parameters are set to be zero. Let's
say that I
>
>The problem with dummy atoms does not lie in sander itself but is a
>statistical effect that makes your results unreliable. Dummy atoms
(on
>both "sides" of the perturbation) can give rise to the origin
singularity
>effect, see for example:
>
>T. Simonson, Mol. Physics, 1993, 80:2,441-447
>
>sander is designed to handle such problems by a modified potential
mixing
>function (setting klambda>1) but that requires to have the dummy
atoms
>only in one state, because the modification that prevents the origin
>singularity for dummies in the perturbed state would make it even
>bigger for dummies in the ground state.
>
>I have tried a code-modification to prevent this, but it is still
work
>in progress.
>
>Kind Regards,
>
>Thomas Steinbrecher
>
>---------------------------------------------------------------------
--
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|