[gmx-users] newbie question about GROMACS input files

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 9 00:30:54 CET 2011

Markus K. Dahlgren wrote:
> 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

The required files are a coordinate file (many formats are acceptable), a 
topology (.top), and simulation instructions (.mdp).

> 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?

These files are only needed by pdb2gmx.  In theory, you don't need them for 
anything if you write a topology by hand.  For instance, for a ligand, it 
doesn't make much sense to incorporate all the new parameters into the 
highest-level force field files just to have pdb2gmx write the same information 
out; just create an .itp for whatever small molecule you have.  pdb2gmx is only 
really useful for macromolecules constructed of smaller building blocks.

> 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?

The ffnonbonded.itp is unnecessary if everything is supplied in the .top - you 
can see how the topology is completely constructed by running through one of the 
many tutorial systems and getting a post-processed topology from grompp -pp.

> 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?

Many coordinate files can be used; a .gro is not specifically required.  You are 
correct about the velocities.  Use "gen_vel = yes" to start a new simulation if 
you do not have velocities you wish to preserve.

> 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.

If you write the topology by hand or with some external software, then you can 
bypass almost everything.



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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