[gmx-users] gmx solvate problem

Alexandr Nasedkin nasedkin at chalmers.se
Wed Nov 8 15:34:04 CET 2017

Hi Golnaz,

Try to increase default VdW radius scaling: option -scale in gmx solvate.

If there are large cavities in ICE you may have problem at water 
interface though.

Best regards,


On 08/11/2017 15:04, G R wrote:
> Hi All,
> I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the
> top and below part of the ice surface with solvent (the solvent is tip4p
> water), some of water molecules go to inside of the ice layers. I did not
> receive any errors, but the coordinate files became messy after salvation.
> I don't know how can I insert water molecules on the top and bellow of the
> surface correctly.
> Thank you in advance for any help,
> Golnaz

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