[gmx-users] galactose bond stretch

Thomas Piggot t.piggot at soton.ac.uk
Mon Jan 17 18:12:22 CET 2011

Whilst this 'problem' you are seeing is probably as Justin has described 
  (a periodic boundary visualisation effect), you should also beware 
when performing carbohydrate/sugar simulations with the default 
parameters in the force field files. If I were you I would check the 
entries against the published parameters (so Lins et al. if you wish to 
use the 45A4 sugar parameters). From my experience then there are some 
mistakes in the parameters in the force field files.



nishap.patel at utoronto.ca wrote:
> Thanks Justin!
>          I am using constraints, but like you said it could be just  
> PBC. I did compare some of my calculations to experimental values and  
> they are fairly similar.
> Nisha P
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> 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.
>> -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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Dr Thomas Piggot
University of Southampton, UK.

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