Hello, Hoping for a positive response... Thank you.
[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&> 05/31/18, 9:26:54 AM --- With Best Regards, Dilip.H.N PhD Student. On Mon, May 28, 2018 at 7:47 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> wrote: > 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.