Hi,
In addition to what Jason said here:
On Thu, Aug 6, 2015 at 7:19 AM, Jason Swails <jason.swails.gmail.com> wrote:
> autoimage
> center :1-374 mass origin
> image origin center familiar
you may want to add an atom mask to the 'image' command so that e.g.
only waters are imaged (otherwise you could potentially re-image the
solute, which you wouldn't want to do at that point).
-Dan
>
> Note that the "familiar" here is because you are using a truncated
> octahedron ("autoimage" takes care of that distinction by default, but with
> the image command it's necessary). In this case, the "autoimage" command
> will properly image the different chains with respect to each other, and
> the following 'center' and 'image' commands will center all of the chains
> in the unit cell and image the waters around that.
>
>
>> autoimage anchor :1-374
>>
>
> If residues 1-374 are from a dimer (i.e., two distinct "molecules"), then
> this is not a good thing to do. If they are imaged in separate boxes, then
> this will prevent them from being imaged back into the same box.
>
>
>> because I've read in the Amber Manual, that autoimage by default center
>> only the first molecule, but after that the water box looked wierd.
>>
>
> You need to be more specific. There are a lot of ways that a water box can
> look "weird". Here are some examples: http://www.shaman.ibpc.fr/heat.png,
> http://ambermd.org/tutorials/basic/tutorial2/files/vmd_crdbox1.jpg (pretend
> that applies to waters), ... and it's impossible to know what people
> consider 'weird' and 'normal'.
>
> One guess I have is that it looks like "chunks" are cut out of the corners
> of the unit cell (like the first link I showed above), in which case that
> problem arises because you did not use NpT to equilibrate the density,
> leading to fictitiously low pressures and a simulation that is actually
> *boiling* as a result. If I am mistaken, you would need to see an image so
> we can see what you see.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Aug 06 2015 - 07:30:03 PDT
