[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 23 17:21:11 CEST 2011

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:


The follow a suitable workflow to add whatever else you need in the system and 
run it:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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