[gmx-users] Vacuum simulation in GMX 5

[Justin Lemkul]

On 5/6/15 12:54 PM, Eudes Fileti wrote:
> Hello,
> in the previous gmx versions I could accelerate simulations in vacuum
> making the cutting cut-offs zero and pbc = no.
>
> However, now it is no longer current possible with GMX 5 (since pbc = no is
> not supported with dd, and the particle decomposition mode is not suported
> in GMX 5).
>
> Does anyone have any tips to speed up a calculation in vacuum?
> I'm decoupling a small molecule in vacuum (for an free energy calculation)
> at a rate of 1ns/h, which seems very slow.
>

That is really slow.  We have been doing some of this lately, and for a 50-atom 
molecule I get 130 ns/day on one core.  Can you post a full .mdp file?

-Justin

-- 
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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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