All,
I have been running simulations using a ReaxFF force field for a DPPC bi-layer. All appears to be going well however I wish to look at order parameter for the lipid chains to gain some insight into the lipid tails and head formation.
I have been attempting to do this through use of a GROMACS tool and playing with file formats, however this does not appear to be working. So I need to find some way to do the calculations though the output of LAMMPS.
I have been trying to find some text on how this is calculated but haven’t found anything that gives enough detail for me to try and calculate it myself.
Does anyone have any suggestions and or references on how to proceed? Maybe any tools for LAMMPS I have not found?
Please let me know if I have over looked something simple or if any data would be useful.
Thank you for any assistance,
All,
I have been running simulations using a ReaxFF force field for a DPPC
bi-layer. All appears to be going well however I wish to look at order
parameter for the lipid chains to gain some insight into the lipid tails and
head formation.
I have been attempting to do this through use of a GROMACS tool and playing
with file formats, however this does not appear to be working. So I need to
find some way to do the calculations though the output of LAMMPS.
what do you mean by "it does not appear to be working"? have you asked
in the gromacs forum.
I have been trying to find some text on how this is calculated but haven't
found anything that gives enough detail for me to try and calculate it
myself.
Does anyone have any suggestions and or references on how to proceed? Maybe
any tools for LAMMPS I have not found?
your chances may be much better, if you ask in a forum where there are
more biophysics people around that actually do use lipid bilayers a
lot, e.g. the CHARMM, Amber, NAMD communities. you may get some raised
eyebrows though, since i would have my doubts about the applicability
of ReaxFF for such systems, and those folks can probably can give you
some tangible reasons for it and not just talk about a hunch like me.
axel.