[gmx-users] progressive imbalance in REMD
Mark.Abraham at anu.edu.au
Sat Apr 14 21:41:27 CEST 2012
On 15/04/2012 3:20 AM, Francesco Oteri wrote:
> Hi Marc,
> 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?
Like I said, look at the end of the .log file.
> 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 ensemble.
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