Hi gromacs users:
I'm simulating a peptide-dppc64 system. When i create my box with
editconf program (editconf -f input.gro -o output.gro -bt triclinic
-c -d 1.5) and i solvate, the molecule go out of the box. I used many
kind of box and some box sizes.
My system size is 4.936 4.408 and 10.503 nm. Should i use -d option
with editconf? I've found in the gmx-users list and in many tutorials,
it should be no less than 0.5.
I don't want to solvate the system in x and y axes due to the
interaction betwen lipids and water. I did it whit editconf -f
input.gro -o output.gro -bt triclinic -c -box 4.936 4.408 12 , but
i didn't use the -d option. Is that ok?
So my question is: Can I do something whit -d and -box option of
editconf program for resulting in a system that it doesn't solvate in
x and y axes, and the molecule isn't out? I need to solvate in z axes.
whould you please help me?
best regard
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