Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules

From: Axel Kohlmeyer (
Date: Fri Feb 21 2014 - 08:11:33 CST

On Fri, Feb 21, 2014 at 9:02 AM, Michal Skoczek <> wrote:
> Hi all,
> I have quite strange problem... I would like to replace atoms (f.ex from C
> (carbon) to N (nitrogen) in multiple molecules of one type in my files. Is
> it possible at all? I just want to change them in already created system
> thats why MOLEFACTURE is not the answer. It allows me to change only
> system up to 200 atoms - mine has 56000.Anyone has an idea how to do it?
> I can provide any details that seem relevant. Any help regarding this
> subject would be greatly appreciated!

should be easy to do with a VMD create a selection of atoms
you want to modify and then simply reset atom name, mass, charge,
type. of course, you have to look up details in the force field
documentation, because you may have to also change the force field
type and (partial) charge of neighboring atoms.


> Many thanks,
> Michal Skoczek
> PhD Student

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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