[gmx-users] LINSC WARNING

Albert mailmd2011 at gmail.com
Fri May 22 15:56:56 CEST 2015

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?

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 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

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