[gmx-users] Warning

[Bratin Kumar Das]

Hi Mark,
            It came from grompp command...in mdp file I have constraint
all-bonds. is it coming due to that.

On Mon, Jul 15, 2019 at 4:57 PM Quyen Vu <vuqv.phys at gmail.com> wrote:

> Hi,
> I think he got this warning due to he did not constraint the H-bond in his
> simulation while he used a timestep of 2fs
>
> On Mon, Jul 15, 2019 at 11:20 AM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > As it says, your time step is too large to be a valid model of that bond
> > interaction. Where did it come from?
> >
> > Mark
> >
> > On Mon., 15 Jul. 2019, 10:32 Bratin Kumar Das, <
> > 177cy500.bratin at nitk.edu.in>
> > wrote:
> >
> > > Dear All,
> > >              I am getting the following error during running REMD
> > > The bond in molecule-type Protein between atoms 49 OH and 50 HH has an
> > >   estimated oscillational period of 9.0e-03 ps, which is less than 5
> > times
> > >   the time step of 2.0e-03 ps.
> > >   Maybe you forgot to change the constraints mdp option.
> > > What could be the reason.....
> > > --
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