[gmx-developers] Reaction Filed crash!

[Miguel Machuqueiro]

Hi again,

It seems that your test was too short for you to see the kind of crashes 
we have been observing.
Right after the first tests we also decided to move to the "v-rescale" 
thermostat. All my latest tests have been done with this and sometimes 
with both (to make sure it was not affecting the results).

A new test using a nstlist=4 and a tau_t=0.05 resulted in a crash after 
2.07 ns. The system distorted on the main chain's NH of the last residue 
of HEWL.

If you care to take a look at my system, here goes the files needed to 
reproduce my crashes:

http://dl.dropbox.com/u/3245083/Lyso_RF-test_GMX-4.5.x.rar

Once again, thank you for all the effort.
Cheers,
Miguel


On 13-12-2011 17:02, Berk Hess wrote:
>  Hi,
>
>  I did one more check. I can run a 128 residue protein for 100 ps with
>  both nstlist=4 and nstlist=5 without warnings. But I do see that the
>  protein is much more above the target temperature than the water.
>
>  One difference I did notice is that you are using a Berendsen
>  thermostat. I would always use the Bussi thermostat (v-rescale)
>  instead. With that thermostat you can make tau_t arbitrarily small.
>  So I would try tau_t=0.05
>
>  Cheers,
>
>  Berk
>
>  On 12/12/2011 09:27 PM, Miguel Machuqueiro wrote:
> >
> > Hi Berk, and all the devel guys.
> >
> > Once again, thank you for not giving up on us.
> >
> > It took me a while to do the tests to check your suggestions and my
> > results are not very famous.
> >
> > A decrease in the nstlist from 5 to 4 was not able to provide
> > stable MD simulations in my HEWL system. All attempts (several by
> > now) ended up in lincs crashed with several stepxxxxxx.pdb files
> > being generated. I also tried simulations using nstlist values of
> > "2" and "1" to be sure: - The system with a value of "2" held on
> > for a while, but eventually crashed after ~15 ns. I reproduced this
> > crash in 3 replicates. - The system with a nstlist of "1" went
> > through the 50 ns test without any problems. Unfortunately, this
> > simulation was very slow; 4 times slower than PME (remember that
> > nstlist=5 gives RF simulations much faster than PME).
> >
> > The idea that RF in previous versions of Gromacs was stable
> > probably due to error cancellation raises in me several concerns.
> > Unfortunately, with the correction in the current implementations,
> > I am not able to use the RF option for the treatment of the long
> > range electrostatics.
> >
> > If you are interested, I could send you the files used to run my
> > tests. Even though we modified our code in order to use GMX version
> > 4.0.7 (in use at the moment), we are still very interested in using
> > the latest and faster versions of Gromacs.
> >
> > Thank you and all the guys doing the hard work! Miguel
> >
> >
> >
> > On 27-11-2011 14:59, Berk Hess wrote:
> >> Hi,
> >>
> >> I found a solution for your problem!
> >>
> >> The basic issue is that a time step for the long range forces of
> >> 5*2 fs = 10 fs is too long in a system where charges move fast
> >> (probably mainly the water hydrogens). With the old,
> >> non-reversible, scheme there must be some cancellation of
> >> errors, which makes the integration stable (although still very
> >> inaccurate). With the new, reversible, integration scheme the
> >> hydrogens in the protein heat up by a factor 1.5 with a
> >> T-coupling strength of tau_t=0.1 (worse than the old scheme)
> >> and they become unstable. Changing the long time step to 8 fs
> >> (nstlist=4 with dt=2fs) reduces the energy drift by a factor of
> >> 4 and makes protein simulations stable. With this 8 fs the energy
> >> drift, for my protein test system, with the new scheme is a
> >> factor 3 lower than with the old scheme.
> >>
> >> The proper solution is using PME. But you said you couldn't use
> >> that for whatever reason. I hope that that is not because you
> >> need pair forces. Note that the reaction field force is NOT a
> >> pair force, it is a collective effect of all charges in the
> >> cut-off sphere, very similar to PME.
> >>
> >> Cheers,
> >>
> >> Berk
> >>
> >> On 2011-11-03 18:52, Miguel Machuqueiro wrote:
>


-- 
============================================
Miguel Machuqueiro
Department of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
Campo Grande, Edifício C8 (sala 8.5.47)
1749-016 Lisboa, Portugal
Tel.  : +351 217500112 (int.ext.28547)
Mobile: +351 967562285
E-mail: machuque at fc.ul.pt
www1: http://webpages.fc.ul.pt/~mamachuqueiro
www2: http://intheochem.fc.ul.pt
______________________________________________


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20111216/c1570d47/attachment.html>