[gmx-users] gromacs genbox SPC water population

Chetan Mahajan chetanvm10 at gmail.com
Thu Jun 26 02:48:31 CEST 2014

Dear All,

I have a system of a crystal slab at the center of the box surrounded by
water. I am using position restraints for crystal. I am observing a weird
thing that after NPT equilibration of system populated with SPC water using
gromacs genbox command, some kinda hole or vacuum appears in the water
layers. Let me explain with the snapshots that can be accessed from
following link:


Image 1 shows equilibrated snapshot of system with "all" as refcoord
scaling option and water NOT from genbox command, but instead inserted
manually. As we can see, there are no holes/vacuum in the box.

Images 2 and 3 show the holes in the water layers. refcoord scaling option
"all" is used and crystal is solvated by SPC water, latter generated using
genbox command.

Image 4 shows equilibrated snapshot of system where "com" option is used
for refcoord scaling, and crystal is populated with SPC water from genbox
command. As we see, there is a displacement of the slab from center to
left, but there are no holes/vacuum in the water layers.

Thus, combination of all option and genbox SPC population is problematic
for some reason. Noting that slab does not move with "all" option, whereas
it does move with "com" option, there is some issue with SPC water
generation using genbox in gromacs. Also, I am using following settle
algorithm for constraining water geometry:

[ settles ]
; i   funct   length-oh length -hh
  1    1        0.1      0.16333

 Could anyone shed light?

Thanks a lot!


More information about the gromacs.org_gmx-users mailing list