Hi, I want to calculate the Spatial Distribution Function of say N-terminal nitrogen atom and all the oxygen atoms of the water molecules. So, i have created the index file in which i have the nitrogen atom and all the oxygen atoms of water molecules. And here are my commands that i gave inorder to calculate SDF: gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact -pbc whole gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit rot+trans gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
I get the following: Reading file nptmd.tpr, VERSION 2016.2 (single precision) Select group to generate SDF: Group 0 ( N) has 1 elements Group 1 ( OW) has 511 elements Select a group: 0 Selected 0: 'N' Select group to output coords (e.g. solute): Group 0 ( N) has 1 elements Group 1 ( OW) has 511 elements Select a group: 1 Selected 1: 'OW' TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c: 5298 TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c: 5298 Last frame 60000 time 30000.000 Back Off! I just backed up grid.cube to ./#grid.cube.1# Counts per frame in all 27 cubes divided by 3.703704e-02 Normalized data: average 1.000000e+00, min 0.000000e+00, max 2.700000e+01 and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it is wired when i give an isovalues and change its values... How can i solve this..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N PhD Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> 05/28/18, 7:47:09 AM -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.