On Wed, Mar 27, 2013 at 10:11 AM, xiao <helitr...@126.com> wrote: > Dear Justin, > Thank you very much for your reply. > I found that the speed of implict MD is slower that explict MD. For > examplex, the speed of an explict MD for a protein of 300 amino acids is > about 3ns per day, however, the implicit solvent is about 1.5ns per day. >
I know. This is what I mean about the need for improving the capabilities of the code. The main point of the implicit solvent approach is that it should be faster. > With respect to the accuracy of implicit solvent, the result shows bad > result. There are two carbon atom types which are not in the gbsa.itp, and > i just copied some carbon atom type in gbsa.itp because i find that there > is no big difference between the carbon parameters. I do not know whether > this is the reason. > You need to establish whether what you did was appropriate or not before you begin accusing Gromacs of being inaccurate. If you observe inconsistencies, errors, poor energy conservation, etc. in the context of some known system, then that might be worth investigating. Problems with a custom topology are more likely to be due to the topology than to the software using it. GB atom types are one possible source of error, but in parametrization, there are plenty of things that can go wrong before you even get to that point. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
