[gmx-users] Diffusion Coeffecient

Nuno R. L. Ferreira nunolf at ci.uc.pt
Mon Mar 21 20:23:38 CET 2005

----- Original Message ----- 
From: "McMullen, Roger L" <RMcMullen at ispcorp.com>
To: <gmx-users at gromacs.org>
Sent: Monday, March 21, 2005 7:05 PM
Subject: [gmx-users] Diffusion Coeffecient

> Hello everyone.
> I would like to calculate the diffusion constant for a system of
> phospholipids.  I have separate trajectory files for each 10 ns of the
> simulation providing a total simulation time of 50 ns.  I would like to
> calculate the diffusion coefficient from the starting time to the end of
> simulation, but do not want concatenate the trajectories as they are
> extremely large.  Does anyone have any suggestions on how I can do this
> properly without concatenation of the trajectories?

When you determine Dt, usually you sub-divide the traj in smaller pieces (do
not remember the flag from g_msd), to get better statistics.
Just do that in each of your trajs.

> Regards,
> Roger McMullen
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