RE: peptides on surface

From: Brian R Novak (bnovak1_at_lsu.edu)
Date: Wed May 13 2009 - 15:25:19 CDT

Jorgen,

You could do this if you don't want to use long range electrostatics or are willing to use a vary large space between slabs. NAMD does not have a 2D or corrected 3D Ewald method to be used with a slab geometry, unless this is being added in 2.7. There is the old multipole method (DPMTA) code that is no longer compiled in the NAMD binaries, but I was never able to get it to compile with 2.6.

Brian

By the way, has anyone succeeded in compiling the DPMTA code with NAMD 2.6 and is it extremely slow?

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu on behalf of Jorgen Simonsen
Sent: Wed 5/13/2009 1:16 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: peptides on surface
 
Hi all,

I would like to simulate 10 peptides and their interactions on a silver
surface - I am not too interested in the beginning to simulate quantify the
interaction from the surface. I am planning to simply freeze the surface
atoms and add a vdw potential to them as I am mainly interested in the
peptide interactions in the beginning. I have not been able to find any
papers using namd for this - has anybody tried?

Thanks in advance

Best

Jorgen

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:03 CST