[gmx-users] gmx solvate problem

Smith, Micholas D. smithmd at ornl.gov
Wed Nov 8 15:38:04 CET 2017

You may want to consider using something a little more powerful than gmx solvate for this, such as packmol (http://www.ime.unicamp.br/~martinez/packmol/home.shtml).

Alternatively, you could construct a layer of water in a separate file and concatenate them together (generate the layer of water in a box with an off-set in coordinates to avoid clashes with where your ice will be).


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Alexandr Nasedkin <nasedkin at chalmers.se>
Sent: Wednesday, November 08, 2017 9:40 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gmx solvate problem

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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