[gmx-users] galactose bond stretch

[Thomas Piggot]

I have added an issue on redmine.

Cheers

Tom

Justin A. Lemkul wrote:
> 
> 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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>>>
>>>
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.