Hi,
On Fri, Aug 7, 2015 at 3:35 AM, Karolina Markowska
<markowska.kar.gmail.com> wrote:
> My 'weird' water isn't shown at any of your examples. It comes out, that my
> 'weird' water was the 'triclinic' water. If I may ask, what's the utility
> of that kind of water representation?
The triclinic shape is what the actual unit cell looks like. You
actually have to do some extra transformations to get the truncated
octahedron shape (which is why 'image familiar' is slower than
'image'). So the triclinic shape is good for speed, while the
truncated octahedron can be "nicer" looking.
-Dan
>
> Thank you once again for your help.
>
> Best regards,
> KM
>
>
>
> 2015-08-06 15:19 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
>
>> On Thu, Aug 6, 2015 at 7:35 AM, Karolina Markowska <
>> markowska.kar.gmail.com>
>> wrote:
>>
>> > Dear Amber Users,
>> >
>> > I have a problem with cpptraj and it's autoimage command. My system
>> > consists of two chains and two Mn2+ ions. I usually use the script below,
>> > but when I use it on this system, something went wrong.
>> >
>> > reference protein_complex.inpcrd
>> > trajin emd2.traj.gz
>> > center :1-374 mass origin
>> > image origin center
>> >
>>
>> These two commands are pointless here. Their effect is promptly
>> overwritten by the "autoimage" command.
>>
>>
>>
>> > autoimage
>> > rms ToRef :1-374.CA,C,N= reference out rmsd_prod.arg mass
>> > atomicfluct out rmsf_prod.arg :1-374 byres
>> > trajout protein_complex_f.binpos binpos
>> > go
>> >
>> > I looks like only the first chain was centered. I've tried to change the
>> > autoimage command and put:
>> >
>>
>> Yes, this is how "autoimage" works. In some cases it can result in a
>> waterbox that looks "shifted" compared to all of the chains, but I have
>> usually found that it suffices for my needs. If you really want all chains
>> to be centered in the box, then you should follow the "autoimage" command
>> with separate center and image commands (the ones I told you were pointless
>> above):
>>
>> autoimage
>> center :1-374 mass origin
>> image origin center familiar
>>
>> 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
>>
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--
-------------------------
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 Fri Aug 07 2015 - 06:30:04 PDT
