Re: namd ( please help me!!! )

From: snoze pa (
Date: Mon Jun 13 2011 - 15:12:19 CDT

Please check NAMD corse grain model tutorail. You may need to modifiy input

On Mon, Jun 13, 2011 at 2:29 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 ?
> 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 –CHxgroups 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!

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