[gmx-users] How to Calculate tetrahedral order parameter
David van der Spoel
spoel at xray.bmc.uu.se
Tue Sep 3 14:35:38 CEST 2019
Den 2019-09-03 kl. 14:02, skrev Soham Sarkar:
> Sorry, I forgot to mention that I have two systems. One consists of
> protein-water and the other one consists of protein-water-urea. I need to
> calculate the tetrahedral order parameter of water around the protein
> within 0.4nm for these two systems.
Sounds like a very difficult problem. I assume you want to evaluate
whether the structure is more ordered close to the protein than in bulk.
In theory you could find all the water molecules with a radius X from
the protein, using gmx trjorder and then generate an index that you pass
to gmx hydorder. However if you use a shell of 0.4 nm there will not be
enough water to test this, and in addition the water interacting with
the protein will not be counted by the program.
The most important question you should ask your self is whether you want
to get out something that can be measured, in that case you would be
better off computing free energies.
> Thanks and regards-
> On Tue, 3 Sep 2019, 5:24 pm David van der Spoel, <spoel at xray.bmc.uu.se>
>> Den 2019-09-03 kl. 13:26, skrev Soham Sarkar:
>>> Dear all,
>>> I know this question was asked by many users before but
>>> them all I did not get how to perform it in GROMACS. Please help me with
>>> this. Is there any in built command line exist for Tetrahedral order
>>> parameter calculation? If gmx hydorder is the existing tool for
>>> tetrahedral order parameter, went through this I did not understand the
>>> usage of it too.
>>> Thanks in advance-
>> What system, water?
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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