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-- David Evans School of Pharmacy University of London ---- Message from david.evans.ulsop.ac.uk at 2005-02-15 17:29:39 ------ >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.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.scripps.edu >>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >> >> >> >--------------------------------------------------------------------- -- >The AMBER Mail Reflector >To post, send mail to amber.scripps.edu >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Tue Feb 15 2005 - 18:53:00 PST