Hi Friends
I am going to use the Amber forcefield of SDS according to the attached paper.
Would you please help me? How can I use the Amber forcefield parameters in LAMMPS?
Thanks alot
Best Regards
Saly
SDS micell size (172 KB)
Hi Friends
I am going to use the Amber forcefield of SDS according to the attached
paper.Would you please help me? How can I use the Amber forcefield parameters in
LAMMPS?
very simple:
- look up the definition of the amber force field
and the details of the exact version of the parameterization
that you plan to use.
- identify the corresponding pair/bond/angle/dihedral/improper
styles in LAMMPS as well as cutoffs, special_bonds settings
and so on.
- create your starting geometry, apply atom types and
look up the corresponding force field parameters.
- with that information you can generate a data and input file
and you are ready to go.
all very straightforward and not overly difficult to do.
cheers,
axel.
Hi Friend
I am going to use the Amber forcefield of SDS according to the attached
paper.
The ability to effortlessly swap from a selection of canned
force-fields with a single command would be very useful.
To this end, I've been thinking about converting some of AMBER's force
field files (like "gaff.dat" or "parm96.dat", or "parm99.dat") into a
new file format which can be read by lammps directly (more or less).
You could in principle, choose from a menu of force-field types at run
time.
(Big Disclaimer: right now at least, it would require using a script,
"moltemplate" which I wrote. Much more on that soon...)
I am wondering if I need to obtain legal permission from anyone to
redistribute these files ("gaff.dat", "parm96.dat"...) in this new
format? I would not mind some help with the file conversion process.
Otherwise it won't happen very quickly. I actually don't need or use
Amber force fields for my research. Feel free to contact me if
interested.)
Would you please help me? How can I use the Amber forcefield parameters in
LAMMPS?
In general, there are many different amber force fields (for example
gaff, ff96, ff98, ff99, ff99SB, and ff03 and others). Clearly you
won't be able to use force-fields which require features which haven't
been implemented yet in LAMMPS (like implicit solvent or polarizable
particles). I'm not familiar with the "ff98" force-field they use in
the SDS paper, but this sounds like your system (in explicit water)
would be possible to simulate in LAMMPS.
very simple:
- look up the definition of the amber force field
and the details of the exact version of the parameterization
that you plan to use.
In addition to reading the papers, here is a (very incomplete list) of
some of the amber force fields parameters and atom definitions used by
amber, which seem to be publicly available:
http://ambermd.org/doc6/html/AMBER-sh-3.html
https://nanohub.org/infrastructure/rappture/browser/trunk/gui/vizservers/pymol/data/chempy/tinker/parm96.dat?rev=699
https://nanohub.org/infrastructure/rappture/browser/trunk/gui/vizservers/pymol/data/chempy/tinker/parm99.dat?rev=699
https://nanohub.org/infrastructure/rappture/browser/trunk/gui/vizservers/pymol/data/chempy/tinker/parm94.dat?rev=699
(I didn't find parm98.dat)
I've no idea how useful these links are, but they seem relevant.
- identify the corresponding pair/bond/angle/dihedral/improper
styles in LAMMPS as well as cutoffs, special_bonds settings
and so on.
For this, take a look at:
- create your starting geometry, apply atom types and
look up the corresponding force field parameters.- with that information you can generate a data and input file
and you are ready to go.all very straightforward and not overly difficult to do.
I know people do this. I suppose it can't be that bad.
I guess everyone has a different pain threshold.
The ability to effortlessly swap from a selection of canned
force-fields with a single command would be very useful.
but is essentially impossible, since all kinds of
force fields have different naming conventions for
atom types and different requirements of what
kinds of atoms you can assign to what type and
how you identify those. at best, you can use the
"generalized" force fields (which trade easier
assignment of force field types for accuracy).
so in order to swap the force field, you'll first have
to convert the atom type naming conventions, but
since this is not always a 1:1 mapping, it is
essentially impossible without a huge database
of complete molecules and residues with preassigned
atom types and a smart matching algorithm.
on top of that, the atom types are only half of
the secret to the assignment. secondly, you
have the per residue charge distribution,
and occasional overrides for bond, angle,
or dihedral force constants and topology
based placement of improper dihedrals.
please have a look at the pdb2gmx and grompp
commands in gromacs, which are probably the
closest to what you are looking for. it would
probably be the easiest approach to try and write
a converter for the topology part of the resulting
.tpr file to a lammps data file and input include file.
i've been pondering to include a reader for gromacs
format .itp files into topotools, at least preprocessed
ones, so far hesitated the effort required and the
responsibility, since people will have a hard time
figuring out, if there are subtle errors.
To this end, I've been thinking about converting some of AMBER's force
field files (like "gaff.dat" or "parm96.dat", or "parm99.dat") into a
new file format which can be read by lammps directly (more or less).
You could in principle, choose from a menu of force-field types at run
time.
that would only work for "compatible" force fields. see above.
(Big Disclaimer: right now at least, it would require using a script,
"moltemplate" which I wrote. Much more on that soon...)
I am wondering if I need to obtain legal permission from anyone to
redistribute these files ("gaff.dat", "parm96.dat"...) in this new
format? I would not mind some help with the file conversion process.
Otherwise it won't happen very quickly. I actually don't need or use
Amber force fields for my research. Feel free to contact me if
interested.)
sorry. am overloaded, too. best of luck,
though. your project is very ambitious.
cheers,
axel.