On 2012-09-20 12:18:02AM -0700, Ladasky wrote: > Hi Peter, > > Thanks for your response. > > Rather than dragging this thread too far off-topic, I'll direct you back to > my thread, where I have just posted additional details. I took a warning > message from GROMACS a bit too literally and it caused me to use conditions > that blew up my simulations. > > I am interested in your protocol for "the typical equilibration." If this > is in fact standardized, do you have a reference? It doesn't match up with > anything in the tutorial files I have been using to run my own simulations. > Admittedly, those files are from GROMACS 3.3, and the procedures may be a > bit out of date. >
Generally it's probably not a good idea to rely on tutorials designed around 3.3 when a google search for gromacs tutorial shows a series of 4.5.x tutorials written by Justin himself, with explanations of why certain steps are conducted. (also when certain features may be implemented differently, such as the introduction of the v-rescale thermostat). -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
