time for every MD step

[Axel]

dear yunfeng,

have you run that input without a thermostat?
does it conserve energy, i think not. you need
to fix that first. remember the GI-GO principle.

your timestep of 1fs is very "ambitious" for
water without any constraints or fudging
with masses.

cheers,
     axel




On Apr 24, 7:20 pm, "LIANG Yunfeng" <liangy... at gmail.com> wrote:
> Wow, I'm the first guy!
>
> Attached are the *.ener file. I thought the input file (attached in the
> previous email) has already contained full information. If necessary, I'll
> send you the coordinates(thanks for your correction) as well. Thanks!
>
> Sincerely, Yunfeng
>
> On Thu, Apr 24, 2008 at 4:38 PM, Teo <teodor... at gmail.com> wrote:
>
> > Dear Yunfeng,
>
> > since you deleted the "coordinations"  (?!?) we can practically do
> > NOTHING.
> > Anyway I suspect that your system is blowing up.. I mean.. your scf is
> > becoming more and
> > more difficult to converge.. probably the problems are really the
> > coordinates (is this what you call coordinations ??)..
>
> > Since you are the first in so many years to observe something like
> > that.. please consider the idea that it could be
> > due to your errors.
> > Or possibly due to kind of miscompilation of the buggy winner prize
> > PGI compiler.
>
> > Can you post coordinates as well? or at least the .ener file?
> > Thanks,
> > Teo
>
> > On Apr 25, 12:20 am, "LIANG Yunfeng" <liangy... at gmail.com> wrote:
> > > See attachment. I just deleted the coordinations.
>
> > > Sincerely, Yunfeng
>
> > > On Thu, Apr 24, 2008 at 4:13 PM, Matt W <MattWa... at gmail.com> wrote:
>
> > > > How much input/output information are you using?
>
> > > > Matt
>
> > > > On Apr 24, 11:06 pm, "LIANG Yunfeng" <liangy... at gmail.com> wrote:
> > > > > Dear Axel,
>
> > > > > it is only a water system. For a small system(with 16 molecules), you
> > > > will
> > > > > only see it (the consuming time increase) after 5000 step(5ps), and
> > > > becoming
> > > > > apparent after 10,000 steps. For a large system(with 192 molecules),
> > you
> > > > can
> > > > > see it around 500 steps. Well, nothing serious...The architecture is
> > amd
> > > > > machine with infiniband and pgi compiler.
>
> > > > > Sincerely, Yunfeng
>
> > > > > On Wed, Apr 23, 2008 at 11:20 AM, Axel <akoh... at gmail.com> wrote:
>
> > > > > > On Apr 23, 12:00 pm, "LIANG Yunfeng" <liangy... at gmail.com>
> > wrote:
> > > > > > > Dear All,
>
> > > > > > > Have you everyone notice the consuming time for Quickstep is
> > > > increasing
> > > > > > as
> > > > > > > the MD is propagating with the time?
>
> > > > > > no. i don't see this. can you provide an
> > > > > > input example...
>
> > > > > > cheers,
> > > > > >   axel.
>
> > > > > > > I guess there will be a way to solve...
>
> > > > > > > Sincerely, Yunfeng
>
> > >  192H2O-md.inp
> > > 2KDownload
>
>
>
>  192H2O-md-1.ener
> 328KDownload