PROGRAM SUMMARY
Title of program:
GenPol
Catalogue identifier:
ADJU
Ref. in CPC:
118(1999)278
Distribution format: uuencoded compressed tar file
Operating system: UNIX, Linux
High speed store required:
1MK words
Number of bits in a word:
16
Number of lines in distributed program, including test data, etc:
7181
Programming language used: Fortran
Computer: Silicon Graphics
Nature of physical problem:
The problem is to place and relax flexible, semiflexible or stiff,
tethered or free model polymer chains within a finite volume with
periodic boundaries such that the configurational statistics is obtained
from a microscopic potential which determines the local and - affected
by concentration and excluded volume - global conformational features of
the system in a 'physical' way. The resulting configuration obeys a
minimum distance criterion.
Method of solution
In a first step, according to the chosen system parameters, a mixture of
phantom and excluded volume chains plus solvent particles are placed
into the (finite and final) simulation box by a Monte Carlo algorithm.
A subsequent molecular dynamics algorithm solves Newton's equations of
motion during the relaxation phase, while the strength of the repulsive
and attractive forces, the temperature and integration time step control
interact with each other by a global optimization procedure which
minimizes the CPU request for the goals i) the minimum distance between
particles is reaching (finally above) its lower limit and ii) the
changes in both local and global conformational properties - as
determined by the Monte Carlo procedure - are kept at a very low level.
The algorithm interrupts the relaxation process when a break off
condition (actually the minimum distance criterion) is fulfilled.
Restrictions on the complexity of the problem
None, except that the machine must provide the needed main memory (see
Sec. 3).
Typical running time
The typical running time increases with the bulk density and the minimum
separation distance and is linearly increasing with system size. The
creation time is of the order of 0.04-0.05 seconds per monomer on a SGI
Octane (R10000, 195 MHz) workstation. See the Sec. 4 'Benchmarking' for
explicit CPU times.