normal To add water molecules

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6 months 6 days ago #9400 by tanvipar123
To add water molecules was created by tanvipar123
I need 20000 water molecules in a lipid bilayer consisting of 246 lipid per bilayer. I did so by increasing z coordinate of the bilayer, and pass the command
$ gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 -radius 0.21, to get 21 thousand molecules of water. But, the 20k water molecules seem to have added on one end of the membrane. How do i distribute them equally?

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6 months 5 days ago #9403 by riccardo
Replied by riccardo on topic To add water molecules
Remember that the system is periodic so what is up is down and what's down is up. Did you try to relax the system (energy min + equilibration)? I would expect the system to quickly equilibrate the water.

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6 months 3 days ago #9405 by tanvipar123
Replied by tanvipar123 on topic To add water molecules
yes, after performing minimization and equilibration, i am getting the final structure with more water molecules on one end.
i also passed this command to overcome PBC
gmx editconf -f bilayer.gro -translate 0 0 3.0 -o translated-bilayer.gro
Is there any way to add as many water molecules we like and distribute them equally across the membrane other than increasing z coordinate of the bilayer?
because it looks like more water molecules have accommodated along Z axis

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6 months 3 days ago #9406 by tanvipar123
Replied by tanvipar123 on topic To add water molecules
yes, after performing minimization and equilibration, i am getting the final structure with more water molecules on one end.
i also passed this command to overcome PBC
gmx editconf -f bilayer.gro -translate 0 0 3.0 -o translated-bilayer.gro
Is there any way to add as many water molecules we like and distribute them equally across the membrane other than increasing z coordinate of the bilayer?
because it looks like more water molecules have accommodated along Z axis

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