[gmx-users] (no subject)

[Justin A. Lemkul]

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

-- 
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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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