Luis Javier Alvarez Noguera wrote:
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?
You seem to have the approach a bit backwards. The choice of force field
is the one which drives everything else, and the basis for that choice
should be what you are hoping to achieve with the simulation. That means
reading literature to see what other people have done, and adapting
their approach to your conditions. A secondary consideration is whether
you have access to suitable tools to generate a suitable physical
description of your starting configuration (for GROMACS, generating the
.top file).
So that takes care of question 1. Question 2 is related to it, but
united-atom force fields can use longer integration timesteps, and are
cheaper to compute per-timestep too. The atom names are chosen by the
force field designers, and you may need to change your input structure's
atom names so that an automatic-topology-generation tool can do the
right job.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
