[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator
gmx3 at hotmail.com
Thu Feb 5 10:48:46 CET 2009
That I have thought about and it would avoid a lot of trouble.
But I have not done that, because that would lead to different run results
every time you rerun grompp, which can be misleading when you are
trying to assess the effects of other parameters.
But maybe the first issue is more important than the second?
Date: Thu, 5 Feb 2009 10:43:22 +0100
From: r.friedman at bioc.uzh.ch
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator
Maybe it's a good idea to have ld-seed=-1 as a default if that's not
already the case.
Berk Hess wrote:
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
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
> 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).
> -- 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.
> -- original message --
> In this manner you use the same random seed and thus noise for all
> 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
> since atoms migrate from one node to another (with domain
> If you do not use checkpoints, use ld_seed=-1 and do not use
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