[gmx-users] gmx_mpi insert-molecules

[shahab shariati]

Dear gromacs users,

I want to do md similation of 10 small molecules in water. To this aim, I
used following commands:

gmx_mpi editconf -f a.pdb -center 0 0 0 -o b.pdb

gmx_mpi insert-molecules -ci b.pdb -o c.gro -nmol 10 -box 10 10 10

I have 3 questions:

1) Is my manner true?

2) For 10 molecules, which dimention of box is appropriate?

3) When I see c.gro using vmd, the part of some molecules are put out of
box.


https://td2ec2in5euwest.teamdrive.net/primespace/public/77350/4MQPVS000T2QS0057UNJ7CHP22TZF9G9/c.gro

https://td2ec2in5euwest.teamdrive.net/primespace/public/77350/TZKXARG00T2QS0057UNJK110Y2TZF9GM/c.jpg

Please guide me about that.

Best, Shahab