From chemistry-request@ccl.net Fri Jun 26 20:11:45 1992 Date: Fri, 26 Jun 1992 20:11 EDT From: tripos!metis!matt@uunet.UU.NET (Matt Clark) Subject: Re: Sybyl FF followon To: uunet!ccl.net!chemistry@uunet.UU.NET Status: RO Date: Fri, 26 Jun 92 16:47:38 EDT Sender: chemistry-request@ccl.net Errors-To: owner-chemistry@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%.