[gmx-users] progressive imbalance in REMD
francesco.oteri at gmail.com
Sat Apr 14 19:20:33 CEST 2012
actually I am running NVT REMD so particle density is more or less
constant along differet replicas.
Is there any way to test which term takes more to be carried out?
Il 13/04/2012 18:02, Mark Abraham ha scritto:
> On 14/04/2012 1:46 AM, francesco oteri wrote:
>> Dear gromacs users,
>> I am running REMD through gromacs 4.5.5 using 10replicas.
>> I am experiencing a problem with simulation efficiency, in particular
>> from gromacs output, like the following:
>> vol 0.49 imb F 4% vol 0.64 imb F 8% vol 0.17 imb F 2% vol 0.56
>> imb F 10% vol 0.17! imb F 7% vol 0.75 imb F 11% vol 0.45 imb F
>> 11% vol 0.13! imb F 8% vol 0.45 imb F 16% vol 0.55 imb F 23% step
>> 735900, will finish Mon Apr 16 07:29:53 2012
>> it seems that higher temperature replicas suffer of an higher
>> imbalance between force and PME.
>> These are the average values:
>> Of course this problem impacts on overall performances.
>> My questions are:
>> 1) Is the progressive imbalance expected?
>> 2) Is there any way to alleviate the problem?
> Guessing wildly in the absence of a description, you're running NPT
> REMD, and so the particle density changes with T, so the nonbonded
> cost varies with T while the PME cost does not. The timing breakdown
> at the end of the individual .log files may prove informative in this
> respect. This problem snowballs - your generalized ensemble can only
> progress at the rate of your slowest contributing ensemble. In theory,
> one could develop a scheme where the PME performance and accuracy was
> near-constant with respect to T by varying the cutoff, splitting
> parameter and Fourier grid, but since most people choose their PME
> parameters by copying people who pulled near-arbitrary numbers out of
> the air, this would seem to be overkill.
> People often do NVT REMD to avoid this effect if they are interested
> only in the ensemble at one temperature. That means the
> higher-temperature replicas have unphysically high pressures, which
> might or might not prove to be useful for enhanced sampling. Some
> people think that makes the sampling at the low temperature bogus, but
> I have never seen a convincing argument that all the replicas should
> correspond to a physical ensemble that closely resembles the target
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