From: Ryan McGreevy (
Date: Mon Aug 11 2014 - 12:24:26 CDT

You can try using the trim or cropping tools found in the 'volutil' plugin
of VMD. These can be limited, however, and will not work if your density
is orthogonal. You can also try tools found in Chimera, which tend to be
more powerful. If you want to fit the density into the simulation box to
avoid NAMD complaining about the map being too big for the periodic cell,
you can suppress this message with the new "gridforcechecksize off"
parameter in your config file (currently only available in nightly builds
of NAMD).

On Mon, Aug 11, 2014 at 4:22 AM, Luba Simhaev <>

> Hello,
> I would like to know how can I fit the target density map into the
> simulated box in a case that they are rotated with respect to each other?
> I saw in the tutorial that it's not supported by VMD. Maybe there is
> another way?
> Thanks!
> Regards,
> Luba