Dear all:
I am trying to simulate small organic molecules with lammps.
For this I am using Accelrys’ CHARMm force field and generate all the necessary files such as topology, parameter and psf files.
According to the README file in the ch2lmp directory these are the files plus crd/pdb I would need to generate the lammps in file.
However, during execution of the perl script I am getting several error messages of missing parameters. I am getting the same
error using a pure protein.
At this point I would not like to discuss the quality of the CHARMm forcefield, I am more interested what the perl script exactly does.
I would have expected a straight conversion into the lammps input format.
Is there anybody out there who knows what is going on or has encountered a similar problem?
Many thanks in advance,
Markus
Dear all:
I am trying to simulate small organic molecules with lammps.
For this I am using Accelrys' CHARMm force field and generate all the
necessary files such as topology, parameter and psf files.
According to the README file in the ch2lmp directory these are the files
plus crd/pdb I would need to generate the lammps in file.
However, during execution of the perl script I am getting several error
messages of missing parameters. I am getting the same
error using a pure protein.
At this point I would not like to discuss the quality of the CHARMm
forcefield, I am more interested what the perl script exactly does.
I would have expected a straight conversion into the lammps input format.
Is there anybody out there who knows what is going on or has encountered a
similar problem?
the conversion that you are looking for is not as straightforward as
you might think, since charmm is doing some things a little different
than LAMMPS and thus the converter has to be a bit "creative".
also, it is likely to be somewhat dependent on the specific version
of the charmm force field parameter/topology files.
while lammps does support "bio" force fields, it is not doing any
of the specific optimizations (e.g. having optimized solvent loops
and analytical constraints for water). thus it is understandable,
that the corresponding support software in lammps are not as
actively maintained as other parts of the package. see the recent
discussions on the msi2lmp converter.
finally, you have to check whether you are using CMAP corrections.
if yes, then you are (currently) out of luck and need to use a different
MD code (or write additional modules to handle this).
in short, many of those contributed tools worked for the person that
wrote them with the input that that person was using, but the longer
ago that was and the less common that type of calculation is done,
the more likely it becomes that you will have to adjust it.
axel.
Paul can comment on the CHARMM conversion Perl script,
as he helped write it.
Steve
Hi Markus. From what you’ve described, and if you’ve followed the instructions in the ch2lmp folder, the script should work. If not, please send the error messages you’re seeing, and your input to me and to Pieter in’t Veld (primary author of the script, CC’d) so that we can take a closer look.
Paul