Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)

From: Wesley Michael Botello-Smith <>
Date: Sat, 23 Jul 2016 09:39:05 -0700

Right. Setting rk2 and rk3 to 0 behaved as expected, but I am trying to get
the restraints to release gradually instead of removing them suddenly. I
was under the impression that the 'value1' and 'value2' flags in the &wt
namelist with 'type=REST' could be used to accomplish this, but they seem
to be getting ignored.
I know that one solution would be to do this over several separate runs,
each I of which has its own .rest file with successively lower rk values,
but this seems quite clumsy to me so I would like to find a better way.

On Jul 23, 2016 7:12 AM, "David A Case" <> wrote:

On Fri, Jul 22, 2016, Wes Smith wrote:
> If, however, I set rk2=0.0 and rk3=0.0, the restrained atoms move away
> rapidly from their starting postion at about 2.9 to a distance of about
> over the 200ps trajectory.

Setting rk2 and rk3 to zero is equivalent to removing the restraint, so the
distance will do whatever it wants. So the behavior has nothing to do with
restraints, and everything to do with the setup and force field used.


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