[gmx-users] SDFs memory allocation error

[Marta Batista]

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?

Thank you.




Marta Batista

PhD student
Department of Chemistry
Campus Universitário de Santiago
University of Aveiro
batista.m at ua.pt