From: Sándor Kovács (skovacs_at_wustl.edu)
Date: Thu Jul 14 2011 - 14:19:52 CDT
Greetings.
This topic may be better suited for the VMD List, but a quick solution
might be as follows:
If you have psf and pdb files for each of your two components
separately, (i.e. one set for your bilayer, and a second set for your
graphene support), you can use "Merge Structures" within "Modeling"
under "Extensions" in VMD.
It will automatically add the two structures together, check for
naming errors, and suggest solutions should any inconsistencies arise.
It will then output a single .psf and .pdb file for you to use in
running NAMD.
When it comes time to run your combined simulation, make sure to have
compatible parameter files for both your components listed in your
NAMD config file.
Things become a little more tricky if you do not have .pdb and .psf
files for your components--for that you will need to obtain or build
them.
Cheers,
Sándor
Ph.D. Candidate
Department of Energy, Environmental and Chemical Engineering
Washington University in St. Louis -- St. Louis, MO 63130 -- USA
On Jul 14, 2011, at 12:31 PM, kanchi subbarao rao wrote:
> hi all
> I have to run NAMD simulations in charmm force field for a
> bilayer with graphene support system. Now I can able to run for
> bilayer simulation.But I don't know how to put graphene as support
> and generate the psf and parameter files for combined system.
> shall anybody sagest me ?
> thanking you all
>
> yours
> subbarao kanchi
>
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