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
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