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