[gmx-users] gmx spatial

Hoda Alibiglou hoda.alibiglou at gmail.com
Thu Jan 26 14:29:59 CET 2017

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,


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