[gmx-users] galactose bond stretch

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 17 17:48:15 CET 2011

nishap.patel at utoronto.ca wrote:
> 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?

You can check bond length distributions with g_bond.  Are you using constraints? 
  Are you sure this isn't just a periodicity artifact during visualization?  If 
the bonds deviated severely from equilibrium values or constraint lengths, the 
simulation would have crashed, so I suspect that what you're seeing is just PBC.


> Thanks.
> Nisha P


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list