[gmx-users] NEMD with sinusoidal pressure variation

David van der Spoel spoel at xray.bmc.uu.se
Fri Jul 21 09:59:15 CEST 2017

On 20/07/17 23:53, Aarushi Bhargava wrote:
> I am simulating a protein using gromacs 5.0.2 and want to apply time
> varying pressure (preferably sine wave) on it. How should I do it in NEMD?
You would have to code to implement a varying pressure of any sort, but 
please think about what kind of physics your are trying to model first. 
Is it all possible to have Ghz or even Thz pressure "waves"? If they are 
much slower you have to simulate not ns or ps but much longer.

Is the pressure coming from air or from a (glass) wall? This may affect 
what you want to implement.

Finally what measurements on proteins (just one?) will you be comparing 
to? This should also influence your design decisions.

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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