VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 03 2011 - 07:10:56 CDT

2011/5/3 Jesper Sørensen <lists_at_jsx.dk>:
> Hello all,
>
>
>
> I want to calculate the solvent accessible surface area in a system with
> many monomers that aggregate. The aggregation occurs across the periodic
> images and therefore the wrapping of the system gets a little complicated.
>
>
>
> Is there a way to make the SASA script/plugin in vmd take the periodic
> images into account when calculating the SASA of certain surfaces?

no. at least not without significant modification of the VMD source code.

>
> I found the below post on the VMD list from March of 2010, but I haven’t
> seen any changes to the SASA script since. Does anybody have an updated
> version that includes the periodic images?

i don't understand. the quoted post is from yesterday and has
nothing to do with SASA.

> I am more than willing to make the code change myself – but I am not sure
> how complicated it would be…

anything with PBC inside VMD is somewhat complicated.

cheers,
    axel.

>
>
>
> Best regards,
>
> Jesper
>
>
>
> --
>
> Jesper Soerensen
>
> Ph.D. student
>
> Dept. Chemistry
>
> Aarhus University, Denmark
>
>
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Saurav Goel
> Sent: 2. maj 2011 02:43
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: VMD- Ra Measurement
>
>
>
> Hi,
>
> I have one question regarding VMD.
>
> I want to calculate surface roughness on top of workpiece which has been
> machined using a tool comprising of silicon atoms and has been imported from
> LAMMPS.
>
> I guess, RMSD tool of VMD will be able to do it. If that's correct, I was
> just wondering what should I select in the RMSD window to do it.
>
> Thanks.
>
> Regards,
> Saurav 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.