[gmx-users] difference of calculation time between the numbers of fep-lambdas values

[Justin Lemkul]

On 4/27/15 1:29 AM, nao.morishita at takeda.com wrote:
> Dear Gromacs Users,
>
> I would appreciate you to give me any comments or hints about the question below.
> What makes the calculation time much longer when I calculate a solvation free energy using the mdp input1 compared to the mdp input2?
>
> Input1
> Free_energy           = yes
> Couple-lambda0        = vdw-q
> Couple-lambda1        = none
> Couple-intramol       = no
> Init-lambda-state     = 2
> Fep-lambdas           = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> Calc-lambda-neighbors = 1
> Input2
> Free_energy           = yes
> Couple-lambda0        = vdw-q
> Couple-lambda1        = none
> Couple-intramol       = no
> Init-lambda-state     = 2
> Fep-lambdas           = 0.0 0.1 0.2
> Calc-lambda-neighbors = 1
>
> It takes three times longer when I write down 36 lambda values compared to 3 lambda values even if there is no difference between mdp inputs other than the value of fep-lambdas and it is a normal free energy calculation not like Hamiltonian replica exchange calculation.
>

In the second case, you're only evaluating the Hamiltonian at the native lambda 
and one other value (as there is only one neighbor).  In the first case, you've 
got two neighbors.  That doesn't explain the big difference in performance. 
Everything else about the run is the same - hardware, number of cores, etc?

Note that without couple-moltype, you're going to be decoupling the whole 
system, which is (1) not what you want for calculating solvation free energy and 
(2) extremely slow.  There is an inherent slowdown when running the free energy 
code, but it should not be so large.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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