[gmx-users] LINSC WARNING
ahmedo047 at gmail.com
Fri May 22 16:46:12 CEST 2015
I haven't tried vsites on GPU. I just used them for the united atom ffs
(espically GROMOS ffs) with reaction field method. Actually I didn't get
good results about the ligand in the system. Maybe the problem was force
field (54A7) I used. Because for GROMOS ffs there is another problem that
is helix melting :).
2015-05-22 16:08 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> On Fri, May 22, 2015 at 3:57 PM Albert <mailmd2011 at 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?
> 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
> > > that is used for simulations with explicit hydrogen atoms
> > --
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