[gmx-users] progressive imbalance in REMD

[Francesco Oteri]

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?


Francesco



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:
>>
>> 4.58991117815
>> 5.5175129881
>> 6.32679738562
>> 7.21887045416
>> 8.1979219038
>> 9.45466733702
>> 10.9115133233
>> 12.5899111781
>> 15.0987095693
>> 19.5630970337
>>
>> 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.
>
> Mark