[gmx-users] Problem with small number of water molecules

ehs esa38 at sfu.ca
Tue Mar 11 19:03:45 CET 2014

Hi gmx users,

I have tried many ways to simulate a relatively long ionomer chain (340
atoms) solvated in about 100 water molecules, but I did not succeeded yet.
The ionomer length is mainly in x direction. For instance, I used the
following commands:

  editconf_d -f conf.gro -bt dodecahedron -box 2 1 1 -d 0.5 -o box.gro

  genbox_d -cp box.gro -cs spc216.gro  -p topol.top -o sol.gro

The number of SOL molecules added is 94. However, it is uniformly
distributed in the box and only exists in the central region of the box. I
ran the energy minimization using sol.gro, but it does not converge to
Fmax<100. I checked the output file and it seems that all SOL molecules have
been shifted to left corner of the box. I hope somebody could help me.

Many thanks,

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