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Previous Next The pso program can perform bond rotations on a single molecule in search of the lowest energy structure. This is done with the -b and -m options. The -b option produces a printout of bond locations and indicates which single bonds are 'rotatable'. The -m option is used to create an optimization file with all possible bond rotational positions of the monomer. You can then perform an optimization of the structures in the optimization file to obtain the results. An example of how to use the -b option with the provided Isoprene.inp file is as follows: ./helper -b Isoprene.inp Use the -b option to ensure that bonds have been correctly identified. Then, use the -m option to generate an optimization file containing all possible bond rotational positions of the monomer. An example of how to do this is as follows: ./helper -m Isoprene.inp 30 Isoprene.opt 200 This creates the optimization file Isoprene.opt from the input file Isoprene.inp, using bond rotational angles of 30 degrees. When the structures in Isoprene.opt are optimized, the file is re-written after every set of 200 structures have been optimized. Before generating an optimization file, consider how many bond rotational positions are possible to ensure that the optimization file to be created will not be too large. For this Isoprene Hydroxy Alkyl Peroxy Radical example, if we rotate bonds by 30 degrees, that gives 360 / 30 = 12 possible rotational positions for each bond. In this molecule, there are 5 rotatable bonds. That gives 12 to the power of 5 or 248,832 possible combinations. Fortunately, one of the rotatable bonds has a methyl group attached, leaving only 12/3 = 4 rotational positions for that case. This reduces the number of possible combinations to 4 x 124 = 82,944. This program automatically detects methyl groups and also removes configurations that do not satisfy minimum inter-atomic distance constraints specified in the input file. Also note that while this program does detect rings, it does not handle them. Ring bonds are therefore labeled as non-rotatable. Before doing a bond rotational search be sure to check that bonds are in the appropriate locations and are identified correctly as single, double, or triple using the -b option. If they are not, manually change the criteria used to identify bonds in the file bondLengths.txt. The format of this file is atomic symbol, atomic symbol, bond type ('s' for single, 'd' for double, 't' for triple), minimum distance-maximum distance, where distances are in angstroms. Note that the bondLengths.txt file was automatically generated from average bond lengths stored in the files averageSingleBondLengthsInAngstroms.txt and averageMultipleBondLengthsInAngstroms.txt using the Perl script updateBondLengths.pl. These average bond lengths were taken from the Handbook of Chemistry and Physics. The updateBondLengths.pl program allows bonds to be 15% larger or smaller than average bond lengths when generating bondLengths.txt. Previous Next |