[gmx-users] newbie question about GROMACS input files

[Justin A. Lemkul]

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

-- 
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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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