[gmx-users] gromacs genbox SPC water population

Chetan Mahajan chetanvm10 at gmail.com
Thu Jun 26 11:46:34 CEST 2014

I have solved this problem, by letting -vdwd option of genbox take its
default value rather than my first value of 0.55.

On Wed, Jun 25, 2014 at 7:52 PM, Chetan Mahajan <chetanvm10 at gmail.com>

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

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