On Apr 13, 2011, at 5:59 PM, Jason Swails wrote:
> On Wed, Apr 13, 2011 at 3:47 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>
>>
>>
>> Minimization went fine, but during equilibration I got this message:
>>
>> ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
>>
>
> Your problem is that you didn't change IFBOX in the %FLAG POINTERS section
> of the prmtop. See http://ambermd.org/formats.html for a description of
> this. 1 is a rectangular box, 2 is a truncated octahedron.
>
> Note that you can also use the command "setbox" in leap to set up a prmtop
> with PBC.
>
> HTH,
> Jason
>
I second the use of setbox in leap to set up your prmtop file for PBC.
Be aware, however, that boxes created with packmol are not relaxed to the
force field, so if you try to immediately go to the final density when
setting the box dimensions, it will not work well AT ALL. In fact, sander
will drop core after only a very few steps. There are two basic approaches
to solving this problem that I know about:
1. Do a series of 1-3 step minimizations, starting each minimization from
the ending coordinates of the one before. (Write restart files every step.)
Each time, you will move the system only a little, but the energy will be
declining. After several (or maybe quite a few more than several)
iterations, you will have a system that can be minimized and equilibrated
normally. Do not try to use an abbreviated equilibration regime, spend
the time to do it cautiously.
2. Make the box quite a bit larger than final size, then bring the system
quite rapidly up to, say 100K, then switch to constant pressure dynamics
to reduce the box size. When the changes have settled down somewhat, you
should be able to begin a regular equilibration regime.
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Wed Apr 13 2011 - 17:00:03 PDT
