VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Fri Feb 15 2008 - 11:44:24 CST

thanks I played w/ pbctool and it does the tricks I want.
and I see that it does resize my box dynamically since the info is in
the DCD (FYI: other MD practitioners it's informative to see how small a
volume change really occurs in time!; I had to scale system to just a
small corner to see any changes in size of box. your results may vary)

but why do I have to
 pbc box -shiftcenter { 4 4 4 }

to get the box centered on the image of the system?
(shouldn't the default centering on the unit cell center the box on the
system)

any reason why they should or should not all be same value?
my system dimensions are
{128.945908 95.184196 127.153168 90.000000 90.000000 90.000000}

so I might expect 4 3 4 would work a bit better...and it does.

I presume this has something to do w/ how I initially set up the
simulation and how the PBC box size evolved during min/eq.
but is there any way to determine the shift value from NAMD output
files?

thanks

Tom

On Thu, 2008-02-14 at 23:05 +0100, Olaf Lenz wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: RIPEMD160
>
> Hi!
>
> Thomas C. Bishop wrote:
> | 1) do the periodic images displayed with (graphics reps -> periodic ->
> | +x ; -x etc....) get the PBD dimensions updated every step when
> | displaying an animation of the trajectory?
>
> When you have loaded the periodic information, then yes. Not all formats
> do actually save this information, but those that do work fine.
>
> | Since there is an exwithin command... how about a pbcwithin command?
>
> That would be a good thing. As far as I understood, the whole periodicty
> issue is currently redesigned, so I think afterwards we will have
> something comparable.
>
> | 3) is there a way to easily display the periodic box size
> | e.g. a "show pbcbox" or "get pbc dimensions" command or some other way
> | to obtain values for the PBC dimensions within VMD if it has read them
> | from the DCD
>
> In fact, there is the "pbctools" plugin that can do all this and more:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
>
> Best regards
>
> Olaf
>
>
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.6 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHtLsstQ3riQ3oo/oRA6nyAJ9rqficcHdowW3xXhDDttSibp4cUQCeIngd
> /QCfF2H4+xHc85DBwqVfHDU=
> =7zjZ
> -----END PGP SIGNATURE----- 

-- 
***********************
*  Thomas C. Bishop   *
*Office: 504-862-3370 *
*CCS:    504-862-8391 *
*Fax:    504-862-8392 *
***********************