Hello All,
I am simulating a DPPC bi-layer and was wondering is anyone had any insight into calculating order parameter for the carbons in the lipid chains.
I know in GROMACS for example there is an included program that does this and I cant seem to find something similar for LAMMPS.
Would the best bet be to do the calculation by hand?
Thanks in advance for any advice or insight,
Hello All,
I am simulating a DPPC bi-layer and was wondering is anyone had any insight
into calculating order parameter for the carbons in the lipid chains.I know in GROMACS for example there is an included program that does this
and I cant seem to find something similar for LAMMPS.Would the best bet be to do the calculation by hand?
why don't you just use the gromacs tool?
LAMMPS can write trajectories in formats that gromacs can read.
axel.
Axel,
That is what I have been working towards now, I just wasn’t sure if that was a legitimate method or if I was taking lazy shortcuts unintentionally.
I am currently doing a run with LAMMPS dumping in the XTC format as described in the manual.
The GROMACS tool I want to use (g_order) appears to read in a topology file and an index file, so I think the XTC format should be fine as I generate an index file? Do you have any insight for g_order or should I post that to the GROMACS list?
Thank you so much for your assistance,
Axel,
That is what I have been working towards now, I just wasn't sure if that was
a legitimate method or if I was taking lazy shortcuts unintentionally.
I am currently doing a run with LAMMPS dumping in the XTC format as
described in the manual.
coordinates are coordinates. if the simulation is done correctly, you
can use whatever tool you want to analyze it.
The GROMACS tool I want to use (g_order) appears to read in a topology file
and an index file, so I think the XTC format should be fine as I generate an
index file? Do you have any insight for g_order or should I post that to the
GROMACS list?
you should check what kind of information is actually required to be
in the topology file for this specific analysis tool. typically, it
would be only atom names, masses and molecular connectivity. thus you
don't need a full topology file, but only a partial one. this can be
constructed with the topotools plugin in VMD. it may need some VMD
scripting, to generate the missing pieces of information, but since
you know your system well, it should not be too hard to generate it.
the alternative would be to build a matching (complete) topology in
gromacs. for as long as the resulting system has the identical
topology as your LAMMPS data file, it should just work.
index files can be generated from the topology.
axel.
Axel,
I was thinking topotools and VMD might help here, I’ve used them in the past to go from pdb to lammps data files and they worked great.
Thanks for the advice and guidance!
Axel,
I was thinking topotools and VMD might help here, I've used them in the past
to go from pdb to lammps data files and they worked great.
well, then it may just require one more command to write out the
LAMMPS compatible topology into a gromacs one. please check the
resulting file very carefully with a text editor to make sure what is
needed is there. you may want to update topotools to the latest
version, or simply update VMD to version 1.9.2, if you haven't done
so.
axel.