kumud agarwal wrote:
I want to do energy minimization of a small peptide (19 residues long)
file (in pdb format).
Can you please tell which tutorial is best for this purpose and which
force field should I use.
Any of these should be fine:
http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use
As for the force field, there is no single "best" option. Each force field has
its own sucesses and failures. You should plan to invest significant time
learning about each of the force fields and deciding which is best for your
application, based on known limitations and the underlying theoretical basis for
it. Choosing a force field is one of the most significant steps in conducting a
quality simulation.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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