Yes, I was actually just looking at that part of the user guide, seems like
it is indeed the solution to the boundary problem. Thanks :)
I noticed also from this section the com(i1, i2, i3) style of syntax which
specifies a center of mass. I tried to use that in my mdin file, changing:
variable
type = DISTANCE
i = (1, 5)
min = 0.0
max = 10.0
resolution = 0.05
end variable
end ncsu_abmd
to
variable
type = DISTANCE
i = (com(1,2,3,4), com(5,6,7,8))
min = 0.0
max = 10.0
resolution = 0.05
end variable
end ncsu_abmd
but this throws an error claiming that it isn't happy about seeing a second
open-bracket in there. I tired square and curly brackets also, but to no
avail. Has anyone used center of masses with collective variables in
AMBER? I imagine it must be quite common?
On Tue, Dec 6, 2011 at 8:51 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Dec 06, 2011, Aron Broom wrote:
> >
> > 2) I ran the water dimer test just using the oxygens for each water and
> the
> > PMF is semi-reasonable, but the entire simulation suffers from the fact
> > that the distance can become larger than the range I'm interested in.
>
> You could use a "flat bottom" NMR-type constraint to keep the O=O distance
> from getting too big, e.g.
>
> &rst iat = 3,6, r1=0.1, r2=2.0, r3=12.0, r4=99.0, rk2 = 0.0, rk3=10.0, /
>
> This (untested!) restraint will have no effect until the distance between
> atoms 3 and 6 gets to 12 Ang, and then the energy will rise quickly,
> pushing
> the two molecules back together.
>
> ....dac
>
>
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Received on Tue Dec 06 2011 - 18:00:04 PST
