On Wed, 17 Dec 2014 08:27:25 +0000
<hannes.loeffler.stfc.ac.uk> wrote:
> You define those two subregions in the other two masks. Naturally
> they can be of different size. How you subpartition the TI region is
> a matter of the input file to pmemd not one of parmed.
Sorry, this is probably misleading. What the manual (section
13.2.2.50, p. 243 in the current Amber14 manual) describes as scmask1
and scmask2 should each be filled with what will be timask1 and timask2
in the input file (except in more complicated situation where more
masks may be needed as described in this section.)
I feel that the manual needs some clarification regarding the terms
"common atoms" and "unique atoms". It looks to me that the tiMerge
entry and the section "Free energies" use two different definitions.
Cheers,
Hannes.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 17 2014 - 02:00:03 PST
