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

[ehs]

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,
Ehsan

--
View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-small-number-of-water-molecules-tp5015086.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.