RE: peptides on surface

From: Axel Kohlmeyer (
Date: Wed May 13 2009 - 16:29:23 CDT

On Wed, 2009-05-13 at 15:25 -0500, Brian R Novak wrote:
> 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

one alternative to consider, at least during the time of testing,
would be the LAMMPS code. when tested on idential (bio) systems
against NAMD 2.6 a couple years ago it was about a factor of two
slower, but it is much easier to set up slab systems and mix-and-match
potentials with it. once you figured out what is needed and how
your system should be set up, you can try to use NAMD again
and benefit from the better scaling and higher efficiency in your
production runs.

i'm currently working on a package in VMD that is supposed to make
manipulating and converting topologies between MD codes easier and
that should be able to help you in the process. for the specific
case NAMD to LAMMPS or vice versa, some parts are still missing,
but a good example case and a user willing to try something out,
are the most important ingredients to have something implemented. ;)


> 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: on behalf of Jorgen Simonsen
> Sent: Wed 5/13/2009 1:16 PM
> To:
> 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

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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