[gmx-users] NEMD with sinusoidal pressure variation

Aarushi Bhargava aarushi at vt.edu
Fri Jul 21 16:56:25 CEST 2017

Hi David,

Thanks for the quick response. I am looking for a pressure wave in air with
a frequency in GHz. I am looking to see the mechanical behavior of
proteins. By implementing a code, do you mean implementing an external
script (such as a code written in python) and then embedding it into the
code for gromacs?


On Fri, Jul 21, 2017 at 3:59 AM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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.
> http://www.icm.uu.se
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