ers. How and where to document this kind of thing so that
> people who need it can find it and those who don't need it don't drown
> in paper is an impossible problem!
>
> Cheers,
>
> Mark
>
> On Wed, Sep 18, 2013 at 8:34 PM, Guanglei Cui
> wrote:
> > It is
6 PM, Mark Abraham wrote:
> Implementation and description of a model physics are two different
> things. You could compute KE of a particle with 0.5 * m * v^2, but if
> the mass is used nowhere else, why wouldn't you pre-multiply the mass
> by 0.5?
>
> Mark
>
> On Wed
alence
> between minor version changes such as 4.0 and 4.6. You need to compile
> a 4.0.x grompp to see if your setup is equivalent, but having done so
> you should be able to use the same inputs to 4.6 grompp and get a
> correct simulation with 4.6 mdrun.
>
> Mark
>
> On Wed, Sep 18,
eed in the new .mdp file to reproduce the first one. Note
> that grompp -c yourold.tpr is the best way to get the same starting
> coordinates.
>
> Mark
>
> On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui
> wrote:
> > gmxdump -om writes out a mdp file based on the tpr, but t
13 at 1:39 PM, Szilárd Páll wrote:
> Hi,
>
> On Tue, Sep 10, 2013 at 2:03 AM, Guanglei Cui
> wrote:
> > Hi Szilard,
> >
> > Thanks again for getting back. You may remember the previous thread I
> > started on regression test failure with icc 11.x compiled bina
sure what's missing here.
On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham wrote:
> No. Theoretically useful, but not implemented.
>
> Mark
>
> On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui
> wrote:
> > Thanks. Is it possible to dump the parameters in the tpr file t
Thanks. Is it possible to dump the parameters in the tpr file to a mdp file?
On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham wrote:
> mdrun -nsteps in 4.6 overrides the number of steps in the .tpr
>
> Mark
>
> On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
> wrote:
> > Dea
eate a mdp file
that best matches the parameters found through gmxdump, but it gives me a
lot of LINCS error. I can upload the mdp file and gmxdump file if you are
kind to help. Thanks in advance.
Best regards,
--
Guanglei Cui
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.g
rs more than three years
> old (icc 11, gcc 4.4) to work seamlessly and produce high performance
> with brand-new hardware and code. That's like working on a Formula One
> car with a flint axe. Installing a new compiler is not rocket science!
>
> Mark
>
>
> On Tue, S
completely disable the GPU detection.
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Sep 9, 2013 at 9:52 PM, Guanglei Cui
> wrote:
> > Dear GMX users,
> >
> > I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2,
> and
> > CUDA SD
ilities of
different nodes. Thanks.
Best regards,
--
Guanglei Cui
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)sub
On Sep 4, 2013 5:16 AM, "Guanglei Cui"
> wrote:
>
> > Hi Szilard,
> >
> > Thanks for your reply. I may try your suggestions tomorrow when I get
> back
> > to work.
> >
> > Feeling curious, I downloaded and compiled gmx 4.6.3 on my home
; On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui
> wrote:
> > Hi Mark,
> >
> > I agree with you and Justin, but let's just say there are things that are
> > out of my control ;-) I just tried SSE2 and NONE. Both failed the
> > regression check.
>
> That'
regression
check with no CPU/instruction optimization normal?
Regards,
Guanglei
On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham wrote:
> On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui
> wrote:
> > Dear GMX users,
> >
> > I'm attempting to compile gromacs 4.6.3 with an older
Hi Justin,
Thanks for the response. Right now, I will just have to get around this by
using a slower code. How do I switch off SSE4.1 and use a different CPU
optimization scheme?
Regards,
Guanglei
On Tue, Sep 3, 2013 at 2:39 PM, Justin Lemkul wrote:
>
>
> On 9/3/13 1:47 PM, Gua
my first time to compile gromacs, which I am not very familiar
with. I wonder if anyone can kindly point out what has gone wrong, and
where to look for hints. Any help is much appreciated.
Best regards,
--
Guanglei Cui
PS: I am aware of a warning about using older Intel compilers with 4.6.3,
bu
16 matches
Mail list logo
