From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Feb 23 2017 - 08:33:24 CST
Sorry, I should update that part of the tutorial. At one time it was
necessary that the map box fit entirely inside the periodic cell due to a
restriction in NAMD, but that is no longer the case. If your map does not
meet this criteria, NAMD will still give you a warning, but it will now
give you an option to ignore the check with the following command:
gridforcechecksize off
On Thu, Feb 23, 2017 at 2:00 AM Luba Simhaev <luba.simhaev0703_at_gmail.com>
wrote:
> Thank you for your reply.
> Shouldn't the box of the grid potential be aligned with the simulation
> box?
> Here what is written in the MDFF tutorial:
> *NOTE:* *If the target map and the box are rotated with respect to each
> other, it may be necessary to resample the target map into a cell that fits
> completely inside the water box, which is not yet supported by VMD.*
>
> Thanks
> Luba
>
> On Wed, Feb 22, 2017 at 5:28 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
> wrote:
>
> So long as the protein and the density map, and the protein and the
> membrane are correctly aligned, there should be no problem with running
> MDFF.
>
>
> On Wed, Feb 22, 2017 at 6:20 AM Luba Simhaev <luba.simhaev0703_at_gmail.com>
> wrote:
>
> Hello everyone,
>
> I'm trying to run MDFF simulation of a protein in a membrane. After the
> rigid body docking of the protein to the density map, the target map (dx
> file) and the simulation box (protein+membrane+water) are rotated with
> respect to each other. Is there a way to change the orientation of the box
> in the dx file with respect to the density?
> I would appreciate your help.
>
> Luba
>
> --
>
> *Luba Simhaev*
>
> *PhD Candidate*
>
> *Chemistry **Department*
>
> *Bar-Ilan University*
>
>
>
>
> --
>
> *Luba Simhaev*
>
> *PhD Candidate*
>
> *Chemistry **Department*
>
> *Bar-Ilan University*
>
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