[gmx-users] newbie question about GROMACS input files

Markus K. Dahlgren markus.dahlgren at yale.edu
Wed Nov 9 00:08:21 CET 2011

Hi all!

I am new to the Gromacs mailing list and just started looking into Gromacs for
MD simulations. I have been working on converting BOSS output into automatic
NAMD input for small molecule ligands and now want to create a similar program
for Gromacs input. I have a question regarding the input files, as I find the
large number of files confusing.

What is the required files to start a Gromacs simulation? Using pdb2gmx you need
a pdb file. To get the parameters, ffbonded.itp, ffnonbonded.itp, atomtypes.atp
and *.rtp are needed? Is that all the files needed if these files completely
describe the input molecules? Also, does the new parameters for the ligand need
to go into the existing parameter files inside the XXX.ff folder? Or how can new
*.itp, *.rtp and *atp files be defined and called upon by pdb2gmx?

I also read about the topology file in the manual. If a topology file would be
written by the program, what other files are needed? The topology would have
all atomtypes, names, charges, bonds, angles, and dihedrals. Would it be enough
to supply a nonbonded.itp file together with the *.top file and the pdb file?

Finally I have a question about the *.gro files. Are they always needed when
starting a simulation? For a new simulation, the last three columns (vx, vy,
vz) can be left out?

Sorry about asking about such trivial matters, but the number of files was
confusing and I was not sure what files were needed if I would bypass the
pdb2gmx step and write the topology file directly.

Thanks in advance for any insight you can offer.


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