[gmx-users] galactose bond stretch

[Justin A. Lemkul]

Thomas Piggot wrote:
> 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.
> 

If this is still the case in the latest release, please file an issue on redmine 
so that it can be fixed.

-Justin

> Cheers
> 
> Tom
> 
> 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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>>
>>
>>
>>
> 

-- 
========================================

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

========================================