[gmx-users] Calculating velocity profile for nanochannel fluid flow

[Mark Abraham]

> Respected all,
> I am currently involved in a project which aims to simulate pressure
> driven
> nanochannel fluid flow through a wall made of hydrophobic and hydrophilic
> patches using GROMACS . I have been able to successfully run the
> simulation
> and have been able to obtain most of the plots necessary to validate my
> simulation . However I have been not able to obtain the velocity profile
> of
> fluid along the channel axis . I cannot figure out which command to use to
> obtain the profile. I would be very grateful if you help me out on this
> matter . My doubt is that whether you require some programming outside
> standard GROMACS capabilities or you only use the postprocessing commands
> of
> GROMACS .

My guess is that you've got a much better chance of someone knowing how to
solve your problem with existing tools if you define "velocity profile of
fluid along the channel axis", i.e. give equations. Section 7.4 of the
manual gives a rough outline of the functionality that exists already.

Mark