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unanswered solvate- water out of box?

  • imankatouzian
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4 years 1 month ago #8446 by imankatouzian
solvate- water out of box? was created by imankatouzian
Dear all,

In the simulation of my protein in water.gro (downloaded for CG) when I get my file solvated.gro as I open it in vmd file I notice that my protein is out of the box what should I do in this respect as I did not have this problem when simulated in all-atom mode?
Also, when I want to neutralize my system, should I do this as in all-tom by
the codes I run in all-atom mode?

gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -p topol.top -nname NA -nn 7 -o solv_ions.gro

So, it is right if I do it after the minimization-vacuum step?

Thanks.

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