[gmx-users] SDFs memory allocation error

Justin Lemkul jalemkul at vt.edu
Fri Sep 20 01:20:09 CEST 2013

On 9/19/13 2:56 PM, Marta Batista wrote:
> Hi,
> I am trying to perform SDFs using g_spatial tool from Gromacs.
> I did all steps, recommended and indicated in Gromacs' manual,
> 1. Use make_ndx to create a group containing the atoms around which you want the SDF
> 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
> 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
> 4. run g_spatial on the .xtc output of step #3.
>   but no matter the atoms of my systems that I choose to see in the SDF, I keep having the problem:
> "Reading frame       0 time    0.000   Memory allocation error"
> As in the manual, they say that this could hapen and we should increase the -nab value. I did it, and I keep having this problem....
> Can anyone help me, to solve this problem?

How large is the group for which you are trying to calculate an SDF (how many 
atoms)?  As I recall, g_spatial requires a lot of memory, so if you have a lot 
of atoms, it may simply not be possible depending on your available memory.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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