Dear Mark,
I've contacted the authors already. I decided to publish here as well just
to close this topic.
Alan
On Wed, Jul 29, 2009 at 13:45, Alan wrote:
> As I found out by test&error myself, mdrun-openmm will not work with
> systems with more than one chain.
>
> Cheers,
> Alan
>
> On Tue, Ju
Alan wrote:
As I found out by test&error myself, mdrun-openmm will not work with systems
with more than one chain.
Please contact the authors with this sort of feedback for them to put in
their documentation. I'm not aware that they subscribe to this list.
Mark
__
As I found out by test&error myself, mdrun-openmm will not work with systems
with more than one chain.
Cheers,
Alan
On Tue, Jul 28, 2009 at 15:04, Alan wrote:
> Dear all,
> Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac
> and Windows so far, and it comes with examples
Dear all,
Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac
and Windows so far, and it comes with examples, pretty neat.
Even though there's some apparently fixes compared to the usual release of
openmm and gromacs-openmm, my molecule didn't work with it yet.
Nevertheless,
Alan wrote:
Thanks Justin.
I could swear I tried what you said... anyway it worked now (2.5 x
faster), but not with implicit solvent for mdrun-openmm... Trying with
plain mdrun with the setup for implicit solvent and it seemed to work
(although I don't know how to interpret this from
GromacsOpen
Thanks Justin.
I could swear I tried what you said... anyway it worked now (2.5 x
faster), but not with implicit solvent for mdrun-openmm... Trying with
plain mdrun with the setup for implicit solvent and it seemed to work
(although I don't know how to interpret this from
GromacsOpenMMPreview3-Mac
Alan wrote:
Ok, I tried.
Can someone tell how to have in a mdp file this combination (in order
to satisfy gromacs openmm) without raising a error in grompp?
ns_type = simple
pbc = no
coulombtype = Reaction-Field
Whatever I try I get:
ERROR: Twin-range neighbour searching (NS) with simple NS
Ok, I tried.
Can someone tell how to have in a mdp file this combination (in order
to satisfy gromacs openmm) without raising a error in grompp?
ns_type = simple
pbc = no
coulombtype = Reaction-Field
Whatever I try I get:
ERROR: Twin-range neighbour searching (NS) with simple NS algorithm
not i
Dear Mark,
Thanks. I reread those file carefully and noticed the "only implicit
solvent". Sorry for that. I am building my test case here to see by
myself how fast it can be.
Alan
On Sat, Jul 18, 2009 at 11:00, wrote:
> Alan wrote:
>> Hi list, does anyone have an example (input pdb, gmx comma
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