[gmx-users] how likely that charmm-in-gromacs LJ-14 interactions are affected by inclusion of cgenff stuff when adding a new molecule with published charmm parameters?

Christopher Neale chris.neale at alum.utoronto.ca
Mon Aug 8 07:05:30 CEST 2016

Dear Justin:

I have another question, this time about LJ 1-4 interactions.
I notice that charmm36-jun2015.ff/ffbonded.itp has the following in [ pairtypes ]

  NH1     S  1  0.316269044940  1.255200000000

and it has the following in [ atomtypes ]

    S    16    32.060000    0.000  A  0.356359487256  1.88280
  NH1     7    14.007000    0.000  A  0.329632525712  0.83680

charmm in gromacs is comb-rule 2, so sigma = aritmetic and epsilon = geometric

For the S-NH1 LJ1-4 interaction, the epsilon makes sense, but the sigma is off.

Am I to conclude from this that charmm uses a whole bunch of semi-arbitrary LJ-14 terms? I checked in gromacs by simply removing the [ pairtypes ] section and when I did that my energy match from gromacs to charmm executable goes from not bad to really terrible (which aligns with the idea of charmm having a bunch of pre-set 1-4 interactions). 

My confusion stems from m reading of charmm mailing list posts in which alex states that modifications of the LJ1-4 scaling is only done in special cases (e.g, https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=1048 )

I ask because I am trying to ensure that the inclusion of all the cgenff stuff in the charmm36-jun2015.ff gromacs distribution is not going to unexpectedly affect LJ1-4 interactions in a molecular modification for which parameters have been published by another group who does their simulations with charmm. In this case, my charmm vs gromacs executable LJ difference goes up from ~ 0.01 kcal/mol for a 200 aa protein to 0.08 kcal/mol simply by adding a ~10 heavy atom covalent acylation.

Thank you,

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