Hi Yeping Sun, If the coordinates are garbled (what are serious coordinate clashes?), you'll have a hard time with either NAMD or Gromacs.
Cheers, Tsjerk On Mon, Apr 13, 2015 at 6:05 AM, sunyeping <sunyep...@aliyun.com> wrote: > > Dear all, > > I modelled a structural model of a complex containing two large proteins. > There are serious coordinate clashes between these two proteins in the > model. Can I expect to do Gromacs simulation to solve the problem of > cooridnate clash and obtain a more rational model? > Best regards, > Yeping Sun > Institute of Microbiology, Chinese Academy of Sciences > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
