[email protected] 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.
-Justin
Thanks.
Nisha P
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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