Joschua Sterzenbach wrote:
Hi
what do I need for a md with gromacs? I made a tutorial in which I
download an example file, but what I I don't have such a file downloaded
from the pdb?
What do I need to create a first input file?
To run a simulation, you need coordinates (.gro,.pdb, etc), a topology (.top),
and instructions to run the simulation (.mdp). Start with getting your
coordinate file:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
The follow a suitable workflow to add whatever else you need in the system and
run it:
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_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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