[gmx-users] LINSC WARNING

[Ahmet Yıldırım]

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

2015-05-22 15:27 GMT+02:00 Vy Phan <phanvy120690 at gmail.com>:

> Thank a lot for your suggestion.
>
> Tuong VY
>
> 2015-05-22 20:21 GMT+09:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > Start by learning what makes a time step stable, e.g. manual 6.8
> >
> > Mark
> >
> > On Fri, May 22, 2015 at 10:51 AM Vy Phan <phanvy120690 at gmail.com> wrote:
> >
> > > Dear Gromacs Users,
> > > When I run npt equilibrium, I set the step  size is 4fs. I go many
> LINCS
> > > WARNING
> > > "bonds that rotate more than 30 degrees"
> > >
> > >
> > > When I reduce the step size to  2fs. All thing is fine.
> > >
> > > Could someone here explain to me?
> > > Finally, I want to use step size is 4fs. Any suggestions for me?
> > >
> > > Thank you
> > > Tuong Vy
> > > --
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Ahmet Yıldırım