[gmx-users] LINSC WARNING
mark.j.abraham at gmail.com
Fri May 22 16:08:46 CEST 2015
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
> 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
> > 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
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