[gmx-users] is there any bug in 4.0.5

[Mark Abraham]

Justin A. Lemkul wrote:
> 
> 
> Nilesh Dhumal wrote:
>> Hello,
>>
>> 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 
>> pure
>> water and glcose + water which is same.
>> Is there any bug in gromacs or I made some mistake or my results are 
>> correct.
> 
> 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.

Mark