[gmx-users] Error during nvt: Not enough memory. Failed to allocate 3425307227 aligned elements of size 4 for grid->grid. What is happening

[Justin Lemkul]

On 4/10/17 8:12 AM, Li, J. wrote:
> This error appeared when I tried to do a NVT simulation. The simulation box
> is 768.00000 768.00000 768.00000 [nm**3], in which there are 90000 atoms.

There's got to be a ton of void space in that system.  90,000 atoms should fill 
a box about 100,000 times smaller.

Regardless, the memory allocation indicates that it needs 12 GB but can't have 
it, so you're just running out of memory.  Either build a smaller system or use 
a machine with more memory.

-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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