Hi, On Fri, May 22, 2015 at 3:57 PM Albert <mailmd2...@gmail.com> wrote:
> that's interesting. > > How about the ligand in the system? The hydrogen should also be treated > in virtual site? Is it possible treat the binding pocket as explicit > atoms, and all the rest in virtual hydrogen? > You're probably thinking of united atoms, which are entirely distinct. You can read all about virtual sites in the manual and publications ;-) Does it support GPU? > Yes Mark thx a lot > > Albert > > On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote: > > Hi Phan, > > > > If you want to use the time step of 4 fs, you can try to use "virtual > > sites" (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the > following > > web site. > > > > https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server > > Virtual sites:The use of virtual sites offers another possibility to > > increase the efficiency of the simulation. These are used to replace > > hydrogen atoms, removing the fastest vibrations in the system that > > otherwise limit the time step that can be used. Simulations run with > > virtual sites can therefore use a time step of 4 fs, instead of the 2 fs > > that is used for simulations with explicit hydrogen atoms > > -- > 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. -- 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.