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
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