Dear Everyone,
I plan to use CHARMM force filed in Lammps for a protein-membrane system. The parameter file I use is CHARMM22 parameter file including phi, psi cross term map (CMAP) correction.
I have 2 points not very clear, after searching the mailing list:
(1) from Lammps doc page on Charmm potential (section 6.3) http://lammps.sandia.gov/doc/Section_howto.html#howto_3
I didn’t find the CMAP energy term and not sure how Lammps deals with this correction term.
(2) My understanding about the converter tool “charmm2lammps” is: it is not able to convert the parameters related to CMAP into Lammps data file. Is this correct?
Thank you very much for your help and time.
Lili
Dear Everyone,
I plan to use CHARMM force filed in Lammps for a protein-membrane system.
The parameter file I use is CHARMM22 parameter file including phi, psi cross
term map (CMAP) correction.
I have 2 points not very clear, after searching the mailing list:
(1) from Lammps doc page on Charmm potential (section 6.3)
http://lammps.sandia.gov/doc/Section_howto.html#howto_3
I didn't find the CMAP energy term and not sure how Lammps deals with
this correction term.
it currently doesn't. there are hooks in the code that would make it
possible, and there is/was somebody working on it, but the CMAP
feature is not (yet) available.
(2) My understanding about the converter tool "charmm2lammps" is: it is not
able to convert the parameters related to CMAP into Lammps data file. Is
this correct?
charmm2lammps hasn't been updated much (it is very difficult to read
and alter) and assumes a rather oldish version of the CHARMM force
field. it doesn't currently support CMAP.
in short, you are out of luck, or looking at a lot of work.
axel.
Thanks Axel for your explanation.
For those (if any) who use Charmm ff (with CMAP) in Lammps, is there any way to overcome such limitations?
What conditions will make CMAP term important regarding the configurations of the bio-molecules?
Many thanks for your help,
Lili
Thanks Axel for your explanation.
For those (if any) who use Charmm ff (with CMAP) in Lammps, is there any way
to overcome such limitations?
well, you have four choices:
- ignore CMAP and essentially use only pre-CMAP CHARMM forcefield
parameters, with the resulting difficulties in credibility of the
resulting work
- implement CMAP or help the person working on implementing CMAP. i
don't know about the status of it, so i cannot say if this is an
ongoing project and if yes, in what state it is and when it will be
available.
- use an MD code that does have CMAP implemented. that is likely to be
more efficient and better tested than LAMMPS for this kind of
simulation anyway.
- use a different force field family altogether that has only terms
which are supported by LAMMPS.
What conditions will make CMAP term important regarding the configurations
of the bio-molecules?
this is best learned from the papers *describing* the CHARMM force
fields, and particularly the CMAP terms.
axel.