[gmx-users] gromacs genbox SPC water population

Chetan Mahajan chetanvm10 at gmail.com
Thu Jun 26 02:52:29 CEST 2014

Just to be complete: I am using following command to populate system with
SPC water using genbox:

genbox -cp slab_wligf.gro -cs spc216.gro -vdwd 0.5 -box 3.081 3.637 11.07514


On Wed, Jun 25, 2014 at 7:48 PM, Chetan Mahajan <chetanvm10 at gmail.com>

> 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:
> https://www.dropbox.com/sh/jms49mz5w409d5p/AACUx7ek7x91Rvv0yiVW2cPEa
> 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!
> regards
> Chetan

More information about the gromacs.org_gmx-users mailing list