[gmx-users] galactose bond stretch

[nishap.patel at utoronto.ca]

Hello,

    I ran a simulation of one molecule of galactose (cyclic) in water.  
After the simulation run, when I checked the trajectory file in VMD,  
the bonds in the galactose molecule stretched and during the run  
changed back to its original starting form. I am using GROMOS force  
field ffG53A6 and parameters as mentioned for carbohydrates in the  
forcefield, so I am not sure what went wrong.I generated topology  
using 'pdb2gmx' command. Also GROMACS did not give any warning during  
the run and my simulation did not crash. Any insights?

Thanks.

Nisha P