Re: [AMBER] TI input files in A9 tutorial and Amber12 manual

From: <>
Date: Sun, 8 Sep 2013 12:56:16 -0400 (EDT)


> For example, in the one-step Mg+2 system, you had an ion-containing water
> box as V0 and the same water box without ion as V1; and both crgmask and
> scmask masks were ':Mg+' for V0 and ' ' for V1. This, both vdW and charge
> interactions for the ion are expected to change from Mg+ parameters to
> nothing. Am I understanding it correctly? And so the integration over
> DV/DL values over the 99 windows on this one step added up to ~414
> (according to table 3), right? 

Almost. crgmask was set to '' in V0 as well, otherwise you strip the
magnesium charge before any calculations start and effectively let an
uncharged magnesium-sized particle disappear.

V0: scmask='MG', crgmask=''
V1: scmask='', crgmask=''

you let a charged magnesium disappear completely, treating both its charge
and vdW interaction via soft-core potentials.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Sun Sep 08 2013 - 10:00:03 PDT
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