David van der Spoel wrote: > Emanuel Peter wrote: >> Dear Gromacs-users, >> >> At the moment I have a question which regards the different >> electrostatic algorithms mentioned in the Gromacs-manual. >> >> I did some simulations and I tried three different electrostatic >> algorithms: Cut-off, Shift and PME. >> >> It is clear to me what Shift and PME means principally, but I ask myself >> which electrostatic algorithm is used by Cut-off. >> I know that Cut-off means a twin-range-electrostatics calculation with >> rlist as the first range and r_coulomb as the second range. Both are >> calculated within different frequencies. Is that true ? >> >> In my .log file it is mentioned that when using Cut-off a default value >> r_coulombswitch equal to 0 is set. It is the same in the case of >> r_vdwswitch. >> >> Does that mean that I use in this special case a switch function which >> switches at 0 nm which represents in this case a shift-function that >> shifts my electrostatic potential in such a way, that it decays to zero >> at r_coulomb? >> I think this means that I used a shift-function which is calculated >> within the twin-range-electrostatics scheme. >> Is this true? >> >> What disadvantages does the twin-range-electrostatics calculation >> have in comparison to PME? >> Is it true that PME could stabilize my system artificially? >> > No, it is the other way around. Cut-offs are bad. > Check: > J. Chem. Theor. Comp. 2 pp. 1-11 (2006) > > >> Now another question: >> >> Some people who perform molecular-dynamics calculations are stabilizing >> the dihedral angles in the forcefield to avoid 'unrealistical' >> fluctuations of their protein. Is this a reasonable way to simulate a >> protein? > No, you are changing the force field in that way. I haven't heard of > this previously. I guess you mean CMAP in CHARMM. You can check out the relevant paper, which also includes details about some other force fields.
Ran. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php