AMBER Archive (2008)

Subject: Re: AMBER: Protein rotating out of box

From: Lars SkjŠrven (lars.skjarven_at_biomed.uib.no)
Date: Wed Apr 02 2008 - 07:36:20 CDT


Hi Steve,
Thanks for your comments. I guess the solvateoct is the way to go
here. However, after I solvate using the command:
'solvateoct mol TIP3PBOX 15.0 0.78' parts of the solute is outside the
box. Hmm.. Does not the buffer argument, in this case 15.0┼, specify
the distance between the wall of the box and the closest atom? Or is
it the distance to the walls in the cubic box, and then it shawes off
the corners no matter if the solute is in the way? I have to make the
buffer as high as 33┼ to get the solute entirely inside the box.
Have a nice day.
LarsS

On Tue, Apr 1, 2008 at 4:55 PM, Steve Spronk <spronk_at_umich.edu> wrote:
> Hi Lars,
>
> I know that using an octahedral box would waste waters, but this is
> definitely the preferable method. It's better to have slower simulations
> with an octahedral box than fast simulations that give you junk, like a
> protein interacting with its own image.
>
> The only other method that I can think of is using a rectangular box as
> before, but you could place very weak restraints on a couple of atoms that
> lie along the long axis (preferably on opposite sides of the protein). That
> way the protein couldn't rotate except around the long axis. However, this
> is nonphysical and may introduce other problems--you'll have to investigate.
> I've never heard of this before, but perhaps you could get away with it.
>
> People do simulations with long straight structures like DNA or fibrous
> proteins. You could see if there are any tricks mentioned in those papers.
>
>
> Steve
>
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Lars SkjŠrven
> Sent: Thursday, March 27, 2008 5:35 PM
> To: amber_at_scripps.edu
> Subject: AMBER: Protein rotating out of box
>
> Dear all,
>
> I am simulating a very nice little protein in a rectangular box with
> different dimensions. Unluckily for me, the solute rotates within its
> box during the simulation such that the longest dimension of the
> solute no longer coincides with the longest dimension of the box.
> Thus, it now spans the whole box, and interacting with its image. Some
> atoms are actually out of the box on both ends. I use default values
> of NSCM. I would avoid using a octahedral box since there will be a
> lot of wasted waters.
>
> Any tips on how to tackle the rotation will be greatly appreciated.
> Have a pleasant day :-)
>
> Best regards,
> Lars SkjŠrven
> Department of Biomedicine
> Universitetet i Bergen
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-- 
mvh Lars SkjŠrven
Institutt for Biomedisin
Universitetet i Bergen
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