[gmx-users] gmx-users

Luis Javier Alvarez Noguera lja at matcuer.unam.mx
Thu Mar 27 23:03:03 CET 2008

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,

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

This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

More information about the gromacs.org_gmx-users mailing list