[gmx-users] Questions about brownian/langevin dynamics of bead-spring polymers
suman at sscu.iisc.ernet.in
Tue Aug 19 19:12:19 CEST 2008
I have just started learning gromacs to implement on a bead-spring
polymer system mainly to study hydrophobic collapse. While I am going
through the manual in detail, I have the following questions/confusions.
1. Which force field would be best to study such a system? Currently I
am using ffG43a2 (with improved dihedrals) on a -C-C- chain.
2. Recent literature suggests using dissipative particle dynamics (DPD)
instead of brownian dynamics. I don't think it is incorporated in
gromacs yet. I have found a software called "DPDmacs", which is closely
built around gromacs with limited potentials. Is that the best
alternative to use? What are the specific uses of three different
methods: Langevin Dyamics, Brownian dynamics, Dissipative Particle Dynamics?
3. This is more related to the physics part of it. Is it possible to
obtain the hydrophobic collapse with simple brownian dynamics of an
aliphatic chain? How is the information of water incorporated except for
the random force and friction term? Which quantity makes the polymer
I would highly appreciate any help in these aspects.
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