[gmx-users] gmx-users

[Luis Javier Alvarez Noguera]

Dear colleagues:
We have the cartesian coordinates of a micelle in xyz format and haven't been
able to build up the .top corresponding file with gromacs package program
x2top. There is a confusion on how to feed this program. Is there a document
or an example where we can clarify thigs such as:
1. When building the micelle by hand, what force fields are needed?
2. When is it advaisable to use united  atoms such as CH3, CH2,  etc. and when
 one should  use  single atoms?
3. How are atoms names related to the force field?

Thanks a lot in advance,
Sincerely


Luis Javier Alvarez
Laboratorio de Simulación
Instituto de Matemáticas, Unidad Cuernavaca
Universidad Nacional Autónoma de México


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