Dear all, 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 hydrophobic/hydrophilic here? I would highly appreciate any help in these aspects. Best regards, Suman Chakrabarty. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
