[gmx-users] Heavy atom - hydrogens bond lengths constraints.

[Dawid das]

Yes, you are right. This is due to limited precision of xtc file. For trr I
don't get the same.
I would never expect such large discrepancies. Thank you very much!

2017-05-06 16:33 GMT+02:00 Jochen Hub <jhub at gwdg.de>:

>
>
> Am 06.05.17 um 15:35 schrieb Dawid das:
>
>> Dear Gromacs Users,
>>
>> I am a bit anxious about the results I get for my simulation of protein in
>> a box of water using CHARMM 27 force field.
>> Namely, even though I use following options to constrain bond lengths
>> between
>> hydrogen atoms and heavy atoms:
>>
>> constraint_algorithm    = lincs
>> constraints                 = h-bonds
>> lincs_iter                  = 1
>> lincs_order                 = 4
>>
>> and I do not use
>>
>> define = -DFLEXIBLE
>>
>> so if I understand correctly I do simulate rigid water molecules, right?
>>
>> Anyway, I observe fluctutations of bond lengths between hydrogen atoms and
>> heavy atoms
>> with amplitude up to 0.020 AA.
>>
>
> Is this possibly due to the limited precision of xtc files? Do you get the
> same when reading the trr file?
>
>
>
>> Is this what I can expect? Also, I can clearly see that my water molecules
>> (TIP3P model) are not stiff.
>>
>> Best wishes,
>> Dawid Grabarek
>>
>>
> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.de/
> ---------------------------------------------------
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