Re: [gmx-users] Genion command not working

Thank you very much your reply its working fine if i decrease distance thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/Genion-command-not-working-tp5010776p5014007.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing li

Re: [gmx-users] Genion command not working

IS IT this problem solved or not??? I am also pacing same problem. srinivas -- View this message in context: http://gromacs.5086.x6.nabble.com/Genion-command-not-working-tp5010776p5013999.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing l

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

Dear sir, congrats..and thank you very much for your kind replys.. I fitted some group also I tried whatever possible ways 1.water and water oxygen 2.groups and total system also Even that group and SDF space

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_spa

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_sp

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_sp

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

I meen after g_spatial calculation done. visualisation problem coming. molecule and SDF surface are overlapping somewhat . why? is this wrong result -- View this message in context: http://gromacs.5086.x6.nabble.com/g-spatial-mergin

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

I meen after g_spatial calculation done. visualisation problem coming. molecule and SDF surface are overlapping somewhat . why? is this wrong result -- View this message in context: http://gromacs.5086.x6.nabble.com/g-spatial-mergi

[gmx-users] g_spatial: merging solvent ond solute:::need some distance

g_spatial 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. 5. Load grid.cube into VMD and