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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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