[gmx-users] galactose bond stretch

Thomas Piggot t.piggot at soton.ac.uk
Mon Jan 17 21:07:42 CET 2011

I have added an issue on redmine.



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
>>>> ========================================
>>>> -- 
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Dr Thomas Piggot
University of Southampton, UK.

More information about the gromacs.org_gmx-users mailing list