VMD-L Mailing List

From: Jesper Sørensen (lists_at_jsx.dk)
Date: Tue May 03 2011 - 06:14:31 CDT

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?

 

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

 

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