[gmx-users] Diffusion coefficient

Dallas Warren dallas.warren at monash.edu
Mon Sep 18 00:06:34 CEST 2017


Don't know exactly how to do it myself, but there will be an option
there where you can specify the z coordinate as a way to break it up
into groups.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 17 September 2017 at 06:05, Sohaib. Mohammed
<sohaibmohammed10 at gmail.com> wrote:
> Any help!
> On Saturday, September 16, 2017, Sohaib. Mohammed <
> sohaibmohammed10 at gmail.com> wrote:
>> Hey Users,
>> I want to calculate the diffusion coefficient using gmx msd. I want to
>> divide the box into slices of 5 A parallel to z axis and calculate the
>> diffusion coefficient for each slice. My question is how to make these
>> slices, I've tried gmx trajconv but didn't work with me. I believe it's
>> quite simple and provided by gromacs, but I am struggling with it.
>> Appreciate any idea on how to make these slices.
>> Thank you,
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