Dear gmx users, I made Spatial distribution function of water around my enzyme, and I got a grid.cube file, when I visualize my output file with VMD I see that water distribution has tendency to one side of enzyme, it means when I change isovalue in VMD the water molecules increase or decrease from one side of enzyme but at last they cover whole the enzyme, here is two question: 1. are my commands and choices true?
echo 12 q | gmx_mpi make_ndx -f md_0_1.gro -o indexp.ndx (12=water) echo 0 0 | gmx_mpi trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_S.xtc -boxcenter tric -ur compact -pbc none (0=system) echo 4 0 | gmx_mpi trjconv -s md_0_1.tpr -f md_0_1_S.xtc -o protein_fit.xtc -fit rot+trans (4=backbone of protein , 0=system) echo 12 1 | gmx_mpi spatial -s md_0_1.tpr -f protein_fit.xtc -n indexp.ndx -nab 300 -bin 0.1 (12=water, 1=protein) 2. how can I remove nonbonded water aroun the protein? I greatly appreciate your kind consideration and very much look forward to hearing from you at your earliest convenience. Best regards, Hoda -- 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.