>
> I think you misunderstand what Carlos said. A good test of convergence
> for REMD simulations is to analyze each replica (NOT each temperature), and
> make sure that each replica contains the same information as every other
> replica (especially the low-temperature sub-ensemble). In 'good' REMD
> simulations, each replica will visit each temperature approximately an
> equal amount of time. If you analyze all of the 314K snapshots from each
> replica, the quantities that you compute (e.g., RMSD distributions, RMS
> fluctuations, average structure, percent folded, etc.) for each replica
> should be equivalent. Technically the same is true for all other
> temperatures, but since high temperatures yield far more available states
> than low temperatures, those are harder to 'converge'.
>
I am confused here. What I did was to sort all frames for 314K from each
replica. The list of sorted for 314K begins as follows replicas 26, 28, 28,
6, 6, 6, 6, 6, 3, 3, 3, 28, 6, ..... where 28 is the highest replica.
Perhaps unnecessarily too high. Then, I examined these frames.
If you start from the same snapshot for each replica, 3700 steps is really
> not enough to ensure that the acceptance ratio is not artificially high ...
>
very sorry, it were 370,000 ( six debug simulations of 60,000 steps each)
Is the interconnect too poor to use 4 nodes per replica? GB typically
> scales quite well
>
If 4 nodes per replica are better than 2 per replica, no problem to use 16
replicas. I also did not mention that there are 16CPUs per each of the 64
nodes.
Why are you making all bonds rigid? I would advise against it, since that
> is atypical for Amber force fields.
>
I'll move back immediately to my common usage.
Great help. Thanks for all
francesco
On Mon, Sep 16, 2013 at 12:31 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Sep 16, 2013 at 5:17 AM, Francesco Pietra <chiendarret.gmail.com
> >wrote:
>
> > As to
> >
> > From: Carlos Simmerling
> > <carlos.simmerling.gmail.com<
> >
> carlos.simmerling.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20remd%20convergence
> > >>
> >
> > Date: Tue, 18 May 2010 06:54:14 -0400
> > Much depends on the initial structures. If all the same, you realy
> > need a second run from different coordinates. If different, the data
> > from all replicas should match. This means that you can extract the
> > temperature data from each replica and they should match. For example,
> > fraction folded at 300k must be the same for replica 1 and 2. This
> > takes some effort to analyze.
> >
> > I assume that for a 32-replicas T-remd in the 314-600K range, the above
> > criterion should be applied at replicas sorted at 314K, if the interest
> is
> > in the system at 314K. Replicas extracted at all other temperatures
> should
> > simply be neglected?
> >
>
> I think you misunderstand what Carlos said. A good test of convergence
> for REMD simulations is to analyze each replica (NOT each temperature), and
> make sure that each replica contains the same information as every other
> replica (especially the low-temperature sub-ensemble). In 'good' REMD
> simulations, each replica will visit each temperature approximately an
> equal amount of time. If you analyze all of the 314K snapshots from each
> replica, the quantities that you compute (e.g., RMSD distributions, RMS
> fluctuations, average structure, percent folded, etc.) for each replica
> should be equivalent. Technically the same is true for all other
> temperatures, but since high temperatures yield far more available states
> than low temperatures, those are harder to 'converge'.
>
> The above is just a test for convergence. When you actually want to
> analyze the data, typically people just extract the ensemble from the
> temperature they're interested in and analyze that ensemble. While this
> throws away all of the information generated at higher temperatures, that
> information is less useful, anyway. Force fields are not validated at high
> temperatures, so the results cannot really be trusted like they can at the
> temperatures that the force fields were parametrized. However, there are
> techniques you can use to 'reweight' the high-temperature data to
> supplement the information you have at low temperatures. A good example is
> the multistate Bennett Acceptance Ratio. [1,2]
>
>
> > I started such a T-remd under GB conditions (abandoning implicit water
> > after Prof Simmerling 2013 paper) and progressively increasing
> temperature
> > for a 34aa peptide under restraining of dihedrals for a short initial
> > stretch (the only portion diffracting enough under X-ray).
>
>
> I'm confused here. GB is implicit solvent (which you claim to be
> abandoning)...
>
>
> > Debug T-remd
> > with 32 replicas and 3700 steps for each replica at ts=0.2 fs (exchange
> > ratio higher than 0.7), thus all rigid bonds, show better folding at 600K
> > than 314K. Although the conformation is unknown, there is a more ordered
> > organization ant 600 than 314K. Is that acceptable in order to go to
> > production?
> >
> >
>
> If you start from the same snapshot for each replica, 3700 steps is really
> not enough to ensure that the acceptance ratio is not artificially high
> since the structures at each temperature may be quite similar to each
> other. If, however, the structures are all different, a 70% success rate
> means you are using too many replicas.
>
>
> > Good exchange (ratio 0.4) also with 16 replicas, however with very little
> > gain of computer time as I am bound to use 64 nodes.
> >
>
> Is the interconnect too poor to use 4 nodes per replica? GB typically
> scales quite well
>
> All rigid bonds is something that for MD in general I dislike, particularly
> > if moving ligands are under scrutiny. What about for such a type of
> T-remd?
> >
>
> Why are you making all bonds rigid? I would advise against it, since that
> is atypical for Amber force fields.
>
> HTH,
> Jason
>
> [1] http://jcp.aip.org/resource/1/jcpsa6/v129/i12/p124105_s1 (defines
> MBAR)
> [2] http://jcp.aip.org/resource/1/jcpsa6/v134/i24/p244107_s1 (MBAR with
> temperature re-weighting)
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 16 2013 - 08:00:04 PDT
