Do you know whether there is a script available/could you recommend any programmes? I’m learning the basics of molecular dynamics and scripting is beyond my capabilities at the moment!
Dear Vanessa
I think you may have underestimated the complexity of the task that
lies ahead of you. If you are certain you want to use LAMMPS, then
here is a list of preprocessing tools here:
http://lammps.sandia.gov/prepost.html#builders
Here are numerous other programs which you should also take a look at:
http://projectaten.org/index.php?project=Aten (works with LAMMPS)
http://sourceforge.net/projects/moleculardynami/ (works with LAMMPS)
If you are considering other molecular modeling software, the list is huge:
https://en.wikipedia.org/wiki/Molecular_design_software
https://en.wikipedia.org/wiki/Molecule_editor
https://en.wikipedia.org/wiki/List_of_molecular_graphics_systems
A few programs that come to mind (in no particular order):
OpenMM, NAMD, GROMACS, HOOMD-blue, TINKER, CHARMM, DLPOLY,
AMBER
Materials Studio
MedeA
YASARA
Shrodinger
I wrote one of the LAMMPS molecule builders on the first list
(moltemplate). It should be already included in the tools directory
that comes with LAMMPS. However there is a trade-off between making a
program that attempts to do be able to everything, and making a
program which is optimized for one type of task. Moltemplate falls
into the former category (so does LAMMPS). Moltemplate has no
graphical user interface. (You have to write text files with a text
editor.) Moltemplate currently can automate the process of assigning
force-field parameters for OPLSAA and AMBERGAFF, but it was designed
with the hope that users could dream up their own force-fields rather
than relying on existing ones.
http://www.moltemplate.org/ (scroll down to see the first example)
There is a detailed example of a coarse-grained polymer here (with
side-chain-beads):
http://www.moltemplate.org/doc/moltemplate_talk_2013-8-07.pdf (slides 21-57)
If you already have a polymer consisting of one atom per monomer
(with coordinates (x1,y1,z1),(x2,y2,z2),(x3,y3,z3),...(xN,yN,zN)) AND
you want to replace each of these particles with an entire monomer
(having multiple atoms). In that case see this example:
http://www.moltemplate.org/images/misc/polymers_follow_a_curve.jpg
http://www.moltemplate.org/images/misc/polymers_follow_a_curve_HR.jpg
You will have to create an LT file which defines your monomer.
(Similar to the first example. You can use ltemplify.py to do it for
you if you have a LAMMPS data file containing a monomer.) If your
polymer has N monomers, you will need to create a text file
("system.lt") with N lines similar to the text in this example
(actually 2N lines because you must add bonds connecting the monomers
together). If N is large the best way to do that is to write a
script. The python script I used to generate the text in this example
is appended at the end of this email.
However I noticed that you say "scripting is beyond my capabilities".
If all you ever plan to do is build and simulate all-atom
biopolymers, (for example), then moltemplate (and LAMMPS) are probably
the wrong tool for the job. There are complete ecosystems of tools
(OpenMM, NAMD, GROMACS, MedeA, AMBER, VMD, Chimera, and many
others...) which can almost completely automate the process of reading
PDB files, adding hydrogen atoms (often missing in the crystal
structures), adding ions, assigning atom charge and force-field
parameters for a wide range of existing force-fields.
If you have acess to AMBER (not free), I remember that there were
numerous tutorials (google "Ross Walker amber tutorials") explaining
how to use the various AMBER tools to simulate all-atom proteins and
nucleic acids.
Either way, figure out what is the best force-field to use, and
find a simulation ecosystem that will help you generate bond and angle
topology and assign force-field parameters appropriate that
force-field type. LAMMPS is not the most user-friendly program. If
you need to generate quick results and you don't have time to learn
LAMMPS, and are afraid of scripting, you might consider one of the
simulation programs above.
Andrew
Do you know whether there is a script available/could you recommend any programmes? I’m learning the basics of molecular dynamics and scripting is beyond my capabilities at the moment!
Then the smart choice would be to start learning MD with simpler systems, where the setup of the initial geometries is simpler.
I am also not sold on the benefit of your approach overall. It is generally much simpler building a full system rather than some parts and expect some tool to fill in the blanks. Doing the second thing can quickly become very complex.
Finally, it is near impossible to do MD simulations without doing some kind of “massaging” of files for pre- or post-processing, which requires some degree of scripting and/or programming. So you will be well advised to pick up some skills in that department soon.
It is rather unlikely that somebody can provide you with a “black box” tool/script that does just what you need. This is doubly unlikely since your description of what you are looking for is rather vague.
Life is the hardest…,
Axel