Dear all,
After minimization and equalizations using nvt (v-rescale) and npt (both
berendsen and ;Parrinello-Rahman), a simulation of mine could run well for
200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002
with the particles communication fatal error.
Fatal error:
2 par
On 4/7/20 5:00 PM, Alex wrote:
Dear all,
After minimization and equalizations using nvt (v-rescale) and npt (both
berendsen and ;Parrinello-Rahman), a simulation of mine could run well for
200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002
with the particles communicat
Thanks Justin for the response.
Please find below the mdp file.
The system is a thin film made out of a epoxy molecule, picture in be below
link, with water on top and bottom of the film. I even sometimes have
the same issue when I simulate the bulk of this system, I mean a cubic box
filled by this
Dear Justin,
Any comment please?
Regards,
Alex
On Tue, Apr 7, 2020 at 5:38 PM Alex wrote:
> Thanks Justin for the response.
> Please find below the mdp file.
> The system is a thin film made out of a epoxy molecule, picture in be
> below link, with water on top and bottom of the film. I even so
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms here.
GROMOS force fields are parametrized assuming all bonds are fixed, so
your constraints should be "all-bonds" not "h-bonds."
I would also suggest you
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
>
>
> On 4/10/20 8:13 AM, Alex wrote:
> > Dear Justin,
> > Any comment please?
>
> Sorry, haven't had power/network for a while due to some bad storms here.
>
> GROMOS force fields are parametrized assuming all bon
On 4/10/20 9:16 AM, Alex wrote:
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms here.
GROMOS force fields are parametri
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote:
>
>
> On 4/10/20 9:16 AM, Alex wrote:
> > Thank you for the response.
> >
> >
> > On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
> >
> >>
> >> On 4/10/20 8:13 AM, Alex wrote:
> >>> Dear Justin,
> >>> Any comment please?
> >> Sorry, haven
On 4/10/20 4:17 PM, Alex wrote:
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul wrote:
On 4/10/20 9:16 AM, Alex wrote:
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul wrote:
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had