[gmx-users] question about non-bonded parameters for CHARMM in GROMACS

Michael Francis Hagan hagan at brandeis.edu
Thu Jul 8 14:48:10 CEST 2010

Dear All,


I am confused about the proper choice of non-bonded parameters for
simulating the CHARMM force field  in GROMACS. With other packages I use
VDW-switch and PME with both VDW and the direct space coulomb cut-off at
1.2 and a neighbor-list cut-off of 1.4.  The requirement in GROMACS that
rlist=rcoulomb seems to make that parameter set impossible (unless one
uses PME-switch, which is recommended against in the manual and not
consistent with the original force field parameterization). I have seen a
suggestion to use rvdw=rcoulomb=rlist=1.2, but grompp complains unless
rlist>rvdw under VDW-switch. That seems like a reasonable complaint, but I
am  new to GROMACS and wonder if I'm missing something.  What is the
recommended set of non-bonded parameters?


Thanks in advance,

Mike Hagan



Physics Department

Brandeis University     





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