time for every MD step

[Axel]

On Apr 24, 9:40 pm, "LIANG Yunfeng" <liangy... at gmail.com> wrote:
> To run cp2k starting a configuration (not from previous ab initio), do we
> need relax the configuration firstly and then introduce a small amount
> random distortions to the position as cpmd does.

i never do this. if you have a good classical equilibration
(i found that SPC/E water is pretty close to DFT water)
you can just run for a short time with rescaling (or in the
case of CP2k you can now use the CSVR thermostats)
until you reach a reasonable good. nose-hoover is actually
not very good if you are far from equilibrium.

> Even though to obtain a fully equilibrated velocity for system takes
> time(0.5ps?). Actually we should not be very worried about the energy
> conservation, you see the last 1000 steps of my *.ener file, which seems ok.
> A drift 0.008 Ry/192 is still physical, isn't it?

no, a thermostat can hide a lot of crap. if you cannot
conserve energy in an NVE ensemble well enough you
are in trouble. i found that already 0.5fs timestep was an
agressive choice for flexible water and 0.25fs a conservative
choice. 1fs would be very aggresive for deuterated water.
(0.7fs would be better). adding shake can allow up to 2fs,
2.5 if you are very aggressive with classical potentials.

> Can you draw some lines related to the optimizing procedure to the
> equilibrium state for cp2k MD user?

???? cannot parse.

cheers,
  axel.
> Sincerely, Yunfeng
>
> On Thu, Apr 24, 2008 at 6:56 PM, Axel <akoh... at gmail.com> wrote:
>
> > 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