Re: Sybyl FF followon



Date: Fri, 26 Jun 92 16:47:38 EDT
 Sender: chemistry-request-: at :-ccl.net
 Errors-To: owner-chemistry-: at :-ccl.net
 Precedence: bulk
 In response to Joe Leonard's questions...
 1) The cutoff is not required for single-molecule or non-
 bounded calculations; the energy is the most accurate if the
 cutoff is set to something larger than the molecule.
 Of course you pay the penalty in time required since the
 number of non-bonded pairs increases.
 For simulations with periodic boundary conditions some kind
 of cutoff is necessary, or Ewald summation is used in some
 programs.
 2) I agree with Damodaran in that 8 Angstroms might not be
 suitable for all cases, but it seems to work for most
 situations. The vdw energy drops off very rapidly and the
 energy difference with and without cutoffs is small.
 I'm an empiricist, so I did some calculations to see how
 big a difference cutoffs make. Here are some energies computed
 for crambin (1crn) with all hydrogens added, without any
 minimization. (TRIPOS 5.2 force field, but Hydrogen vdw radius
 is 1.2 Angstroms; Kollmann all-atom charges, constant
 dielectric)
 SYBYL, like AMBER uses a residue-based cutoff; if any atom in
 a residue is within the cutoff distance from another, all
 atoms in both residues are used in the non-bonded calculations.
 Cutoff	vdW E		Electrostatic E		# pairs
 100	691.245		-2684.925		197,287
 8	692.740		-2683.961		 91,773
 The 100 Angstrom cutoff takes about twice as long and increases
 the accuracy by about 0.2%. Bernard Brooks did a lot of work
 to see how different cutoffs affected dynamics trajectories.
 I believe this is what Martin Norin is referring to.
 3) There has been one change since the TRIPOS force field
 paper, involving the handling of hydrogen bond pairs. In the
 paper the vdw term for the two atoms forming the hydrogen
 bond was set to zero so that the two atoms can move closer
 together and lower the electrostatic energy. We found that
 in dynamics the two atoms involved in the hydrogen bond had
 a tendency to "fuse" so that the coulombic energy was
 infinite; now we  scale down the sum of the vdw radii used
 in the vdw term by 70%.