On 9/11/2011 10:08 AM, 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
a pdb file. To get the parameters, ffbonded.itp, ffnonbonded.itp, atomtypes.atp
and *.rtp are needed?
To generate a topology pdb2gmx requires .atp and .rtp files, and maybe
some other stuff depending on what functionality is required. To use a
topology, grompp requires that the #include statements generated by
pdb2gmx make sense, so the .itp files are only then required. Updating
residuetypes.dat can be wise.
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?
You can make a new local copy of the xxx.ff folder and modify that.
However, it is more work to create an .rtp entry for a small molecule
and use pdb2gmx than it is to write a molecule.itp file directly (see
example in Chapter 5 of the manual). Such an .itp file can probably have
[nonbond_params] or [atomtypes] fields in it, or implicitly refer to a
modified ffnonbonded.itp.
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?
Yes. Note that parameters for bonded interactions can be provided
directly in the .itp where the interaction is defined, rather than by
reference to a bonded interaction type entry.
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?
A coordinate file is required, but its format can be to suit your
convenience. Particularly if you are generating velocities, the velocity
values can be irrelevant.
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.
You can.
Mark
Thanks in advance for any insight you can offer.
Best,
Markus
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