[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

[Ran Friedman]

Hi,
Maybe it's a good idea to have ld-seed=-1 as a default if that's not
already the case.
Ran.

Berk Hess wrote:
> Hi,
>
> I don't know why I did not add checks for ld-seed before.
> Now grompp gives a note when continutation=yes and ld-seed!=-1.
>
> tpbconv will now generate a new ld-seed when reading a trajectory
> (but you should not use tpbconv, use a checkpoint file instead).
>
> But yesterday I forgot to tell that there is a bug in the checkpointing
> of mdrun in 4.0 - 4.0.3. Without domain decomposition the initial box
> size would always be stored in the checkpoint file, which causes problems
> with NPT simulations. NPT simulations with domain decomposition and
> all NVT simulations were fine.
>
> Gromacs 4.0.4 will all bugs fixed and extra checks should be released
> today.
>
> Berk
>
> > Date: Wed, 4 Feb 2009 19:30:47 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] micelle disaggregated in serial, but not
> parallel, runs using sd integrator
> >
> > It appears as if you were correct Berk. I will report on the results
> of my 24h test tomorrow, but I also set up another system
> > that used ld_seed=1993 and ran in 20 ps segments instead of the 200
> ps segments that I was previously using. This system shows
> > signs of disaggregation on the 200 ps time-scale as opposed to the 2
> ns time-scale that I observed for 200 ps segments.
> >
> > I don't know how you figured that one out, but I am very grateful.
> >
> > Now that I see the trajectories, it does make sense that any net
> movement applied to an individual molecule by the noise will
> > lead to directed movement over many separate segments.
> >
> > I think this is probably worth a note in the grompp output for sd
> runs when a user sets ld_seed to something other than -1 and
> > utilizes the -t option (or some other indication that this is
> intended as a continuation).
> >
> > Chris.
> >
> > -- original message --
> >
> > Thank you Berk,
> >
> > I will repeat my runs using the checkpoint file and report my
> findings back to this list. Thank you for this advice.
> >
> > Chris.
> >
> > -- original message --
> >
> > Hi,
> >
> > In this manner you use the same random seed and thus noise for all
> parts.
> > In most cases this will not lead to serious artifacts with SD,
> > but you can never be sure.
> > When checkpoints are used, you do not repeat random numbers.
> > This also gives a difference between serial and parallel in 4.0.
> > With serial you get exactly the same noise per atom, in parallel not,
> > since atoms migrate from one node to another (with domain decompostion).
> >
> > If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv.
> >
> > Berk
> >
> >
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