On Tue, Jul 2, 2013 at 10:51 AM, Melchor S. <msm...@cid.csic.es> wrote:
> Hi Tsjerk, > > I read the sae that you say about the PME and the twin cutoff, but as I > have seen that a lot of studies in that people use Gromos with PME and a > Vander Vaals cutoff so small as mine, I didn't change it, for mantain the > same settongs than in OPLS simulations. > > Force fields are very sensitive to these settings, and the value of rvdw is particularly significant. With PME, rcoulomb is more flexible, but I generally do not change rvdw. Recent studies have indeed shown that PME is superior to RF for the Gromos96 force fields, or at least 53A6. > About the structures are very similar, in principle, as I can see in VMD > and > so on, but for sure I will try your suggestions. > > "Similar" is in the eye of the beholder, and without some numeric definition (e.g. backbone RMSD between structures), I'd be wary of defining the results as such. Also realize that force fields are not created equal; all have caveats, some more pronounced than others. I would not necessarily assume that two force fields produce equivalent results, and part of the assessment that one must do (before simulating) is to see who has used what to study what :) -Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- 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
