VMD-L Mailing List

From: Charles Cleveland (charles.cleveland_at_physics.gatech.edu)
Date: Sat Apr 28 2007 - 16:02:55 CDT

I observe that 'pdb' does not show up in a search of the VMD 1.8.6
manual. Where is one supposed to learn about the existence of such
useful facilities? Perhaps there are others that should be publicized.

Olaf Lenz wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: RIPEMD160
>
> Hi!
>
> Jianhui Tian wrote:
>
>> I am simulating a box of water using periodic condition with constant NPT.
>> Here I want to get all the residue LIST of molecules within "x" of resid
>> "b"
>> by using "[atomselect top "within x of resid b"] get resid". If this
>> molecule with resid "b" is on the edge of the unitcell, whether the LIST
>> will contain the molecules whose periodic images are within the
>> distance. If
>> not? How can I do this? Thanks a lot.
>>
>
> Another simple approach would be to use the function "pbc wrap" like
>
> pbc wrap -center "resid b"
>
> to wrap all atoms into a box centered around resid b, and use your
> expression afterwards to select the residues.
>
> Best regards
>
> Olaf
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2 (GNU/Linux)
> Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org
>
> iD8DBQFGM494tQ3riQ3oo/oRA+h8AJsHm0QsanBe34N141gg5GhSu1aPPACgh7p5
> vqj/DBePKp7hMh75vGGUP+g=
> =718h
> -----END PGP SIGNATURE-----
>
> 

-- 
Life would be so much easier if we could just look at the source code.
------
Charles Cleveland, School of Physics, Ga Tech, Atlanta, GA 30332-0430
charles.cleveland_at_physics.gatech.edu                             
    404-894-5219