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? 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? Is it also reasonable to heat up a crystal -.pdb structure, determined by x-ray, slowly from 50 K up to 300 K in a couple of steps? Does this have any purpose or is this just a non proven setup of my structure? Thanks for your good advice in advance! Best regards, Emanuel Peter Institute of Phys. and Theor. Chemistry 93053 Regensburg Germany _______________________________________________ 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
