Hi everyone,
I have a lipid bilayer system of 100 DPPE lipid molecules per leaflet. I want to insert 100Na ions and 100 CL ions per leaflet. The system has the following dimensions in nm: 7.68 x, 7.68 y, 8.5 z. I assume that the limit position that ions can reach is the position of P groups. Considering this, the mean positions of P groups for each leaflet are 57.54856 A and 27.19626 A. In this way, the .dat file for each ion is the same and has 100 lines with the following coordinates for the bottom leaflet: 3.8405728750000003 3.8405728750000003 1.1854. For the top leaflet, the file has this coordinates: 3.8405728750000003 3.8405728750000003 7.30848. Finally, I'm using the following commands to insert the molecules :
gmx insert-molecules -f solvated.gro -ci sod.gro -ip ions_top.dat -o solvated_posionstop.gro -nmol 100 -dr 3.84057 3.84057 1.19151 -try 10000
gmx insert-molecules -f solvated_posionstop.gro -ci sod.gro -ip ions_bot.dat -o solvated_posionsbot.gro -nmol 100 -dr 3.84057 3.84057 1.1854 -try 10000
gmx insert-molecules -f solvated_posionsbot.gro -ci clo.gro -ip ions_top.dat -o solvated_nionstop.gro -nmol 100 -dr 3.84057 3.84057 1.19151 -try 10000
gmx insert-molecules -f solvated_nionstop.gro -ci clo.gro -ip ions_bot.dat -o solvated_nionsbot.gro -nmol 100 -dr 3.84057 3.84057 1.1854 -try 10000
However, it only inserts 98 cations and 97 anions in the top leaflet and 2 anions and 3 anions in the bottom leaflet.
Thank you in advance.
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