Hello Jason,
thank you for your quick reply and help.
Do you think maybe that constant *force* steered-MD would work for multiple
steering paths? Section 4.8.3 of the amber12 manual (pages 149-150) seems
like this should be the case, if we can set more than one path (manual:
"there must be at least one reaction coordinate in this section") . I
tried the example mdin file add-on on page 149 with only one path as a
test, but amber just did the MD simulation, and didn't create any smd.txt
files....
&cntrl ...etc...
/
ncsu_smd
output_file='smd.txt'
output_freq= 1
variable
type = DISTANCE
i = (148998 ,179343 )
path = (X,30 ) path_mode = LINES
harm = (5000)
end variable
end ncsu_smd
On Fri, Aug 24, 2012 at 11:51 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Aug 24, 2012 at 11:39 AM, e g <eg.ug.pl.gmail.com> wrote:
>
> > Hello,
> > I would like to run a steered-MD calculation with amber, using
> several
> > distance constraints simultaneously (i.e. steered to decrease several
> > different distances at the same time). Is this possible? Or can there
> only
> > be 1 steered distance? When I attempt to submit such a run with the
> > below-listed input files, either the 1st constraint is accepted, and the
> > rest are ignored, or I get the following error:
> > ----------
> > "application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0"
> > "In Jarzynsky runs, there must only one restrain, stopping program"
> >
>
> This would suggest only one restraint is allowed (which is confirmed in
> tests that I've recently seen).
>
> What I would suggest doing is setting up a steered MD simulation whose
> reaction coordinate is not a simple distance, but rather a linear
> combination of multiple distances. For instance, for a proton shuttle
> between two atoms, you may make the reaction coordinate the difference
> between two distances (the distance between the H and the atom it's
> transferring TO minus the distance between the the H and the atom it's
> transferring FROM).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Aug 24 2012 - 13:00:04 PDT
