dcip1101 wrote:
Dear all,
I am a new user of Gromacs. To start my job, I am confused by several
questions about GROMACS and requesting the answers.
1. Can one use amber force field in gromacs?
Yes. See http://chemistry.csulb.edu/ffamber/ and follow the usage instructions
carefully.
2. How to prepare parameters for a cofactor not included in the standard
force fields?
This is a very advanced topic. See here:
http://wiki.gromacs.org/index.php/Parameterization
3. Any further suggestions to a new user to use the package better?
Depends on what you are doing. Read lots of tutorials and consult the mailing
list archive and wiki site (wiki.gromacs.org) if you have problems or are not
certain how to implement certain features.
-Justin
Thanks so much for your time.
Have a nice day.
----
Jeffrey
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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