[gmx-users] how to fix molecules and give different temperature

Santan William gmxwilliam at gmail.com
Wed Jul 16 17:33:59 CEST 2008

Dear users,
        I want to do a simulation as below configuration:


        3 boxes are contacting with their neighbors in x direction. BOX1 and
BOX2 are ice crystal, BOX3 is water. I want to fix molecules in BOX1  and
BOX3, so they will not move during simulation. And BOX1 and BOX3 will be
given a different fixed temperature, BOX2 will be given a initial
temperature.So BOX1 and BOX3 will have a temperature gradient. According to
heat transfer theory, the ice in BOX2 will melt from right to left. I want
to observe the melting front moving during the simulation.

        Thus, my questions are:
        1. How to fix some molecules in their position? My case is to fix
molecules which are in left and right.

        2. How to give different and fixed temperature to fixed molecules?
My case is to give fixed temperature to molecules in left and right?

        3. How to give a initial temperature to a part of molecules? My case
is to give initial temperature to the middle molecules.

       Thanks in advance.

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