[gmx-users] galactose bond stretch

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon Jan 17 18:04:35 CET 2011

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
> 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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