[gmx-users] is there any bug in 4.0.5
Mark.Abraham at anu.edu.au
Sun Oct 25 01:15:19 CEST 2009
Justin A. Lemkul wrote:
> Nilesh Dhumal wrote:
>> I am trying to run a simulation of glucose in water using Gromacs
>> 4.0.5 version. During equilibration gulcose was at the centre of the box
>> surrounded by water molecules. In the final results the gulcose come to
>> the one side of the box (behaviour like hydrophobic). I ploted rdf in
>> water and glcose + water which is same.
>> Is there any bug in gromacs or I made some mistake or my results are
> This is not a bug. It sounds more like your parameters for glucose are
> too hydrophobic.
If the box is periodic, there is no "side" for a hydrophobic molecule to
prefer. Neither must it stay in the center. You can use trjconv to make
it look how you prefer.
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