Hello
When I put pdb file from gmx cluster in gmx anadock, gromacs gave error that it
cannot find pdb files while my cluster pdb file involve 40 pdbs in one file.
I was wondering if you could give me some advice.
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Gromacs Users mailing list
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That suggest there is an issue related to the CUDA FFT library -- or
something else indirectly related. Can you use a newer CUDA and try to see
if with -pmefft gpu you are still getting a crash?
--
Szilárd
On Mon, Nov 12, 2018, 11:58 AM Krzysztof Kolman >
> > Dear Benson and Szilard,
> >
> >
Hi,
Ah I see. So unless your hydrated uranyl is modelled with bonded
interactions between uranyl atoms and water atoms, the only bonds in the
system are silicate hydroxyl, water, and uranyl. If so, then I suspect the
default value of lincs-order (which is 4, to suit highly connected
biomolecular
Hi,
On Thu, Nov 15, 2018 at 1:54 PM Kovalskyy, Dmytro
wrote:
> The error you saw is clear evidence of a bug. There's a few things you
> might try to help narrow things down.
> * Is the error reproducible on each run of mdrun?
>
> Yes
>
>
>
> * 2018.3 was not designed or tested on CUDA 10, which
The error you saw is clear evidence of a bug. There's a few things you
might try to help narrow things down.
* Is the error reproducible on each run of mdrun?
Yes
* 2018.3 was not designed or tested on CUDA 10, which was released rather
later. If you have an earlier CUDA, please see if
Dear Gromacs Users
I am trying to simulate glucose molecule and for that I am utilizing the
gromos53a6carbo ff downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields.
After an successful energy minimization step, the NVT equilibration is
throwing error messages and the
Thank you very much Justin for your reply
-Mensaje original-
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
En nombre de Justin Lemkul
Enviado el: miércoles, 14 de noviembre de 2018 14:51
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] pcoupl Berendsen
On 11/14/18 5:28 AM,
Actually the clay has the clayFF force which has only bonds on OH units,
the rest of atoms are just LJ spheres with a charge. I guess the conclusion
is still the same?
On Wed, Nov 14, 2018 at 8:47 PM Mark Abraham
wrote:
> Hi,
>
> On Wed, Nov 14, 2018 at 3:18 AM Sergio Perez
> wrote:
>
> >
