Re: namd ( please help me!!! )

From: Axel Kohlmeyer (
Date: Mon Jun 13 2011 - 14:36:24 CDT

On Mon, Jun 13, 2011 at 3:29 PM, Namd Namd <> wrote:
> Dear Namd experts,
> I have to overcome some problems about force fields immediately to perform
> md via Namd. So I urgently need your help. Could you please help me out ?

if you don't get an answer to a question, it is more likely
that people either didn't understand it, or were not compelled
to answer, e.g. because you are asking something that is
self-evident or could be easily answered by looking into a
textbook or alike. stating your urgency on top of that
doesn't help. on the contrary, it usually makes it even
less likely to get a competent answer.

to improve your chances for an answer, you should think
about reformulating your questions so that it is easier to
understand what you are asking for and perhaps make
a better effort to try and answer them yourself.



> By using CHARMM19 force field, I am trying to simulate the binary mixture
> consisting of A and B type molecules. I have some questions about topology
> and parameter files.
> 1. The first line of topology file
> 19 1
> indicates CHARMM19 force field, as it is known. Is it possible to model the
> molecule A in the mixture  with united atom model that treats –CHx groups as
> single interacting site and the  molecule B  with all atom model that treats
> each atom as a site?
> 2. In topology file, the line
>    atom N1   NYZ  -.56
> implies the atom with the name N1,  the type NYZ, and a charge of -0.56. If
> NAMD automatically generates the angles and dihedrals according to the atom
> types defined in topology file, I think that the atom types have to be
> taken from CHARMM19 force field. But I am not sure that. Do the symbol for
> atom type (in my topology file NYZ) have  to be one of the CHARMM19 atom
> types or is any  other  userdefined symbol (like NYZ)  possible?
> Thank you all for the responses.
> Best regards!

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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