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 batist...@ua.pt -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
