>
> I'm confused here. GB is implicit solvent (which you claim to be
>
abandoning)...
Sorry, I intended to write "explicit water"
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 - 08:30:02 PDT
