Dear Justin, Thank you very much for your suggetions. BW Fugui
At 2013-03-27 22:15:23,"Justin Lemkul" <jalem...@vt.edu> wrote: >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 -- 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