[gmx-users] progressive imbalance in REMD

[Mark Abraham]

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.

Mark

>
>
> 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
>