[gmx-users] diffusion coefficient with g_msd

Sarah Witzke sawit02 at student.sdu.dk
Thu Jun 4 16:18:22 CEST 2009

Dear gromacs users,


I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer.

I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual pages) that g_msd uses the Einstein relation. Reading "Molecular Modelling: principles and applications" 2.ed. by Andrew Leach it is explained that the "for calculating the diffusion coefficient the mean-squared distances should not be limited by the edges of the periodic box. In other words, we require a set of positions that have not been translated back into the central simulation cell." This makes sense since I try to calculate the distance a molecule diffuse.

I haven't been able to find any mention of how gromacs handle this either in the manual or on the wiki page. The search function on the old webpage directs me to the new webpage, which doesn't give any results for "g_msd" or "diffusion coefficient" or alike, so my apologies for asking a question I could have found the answer to I old emails. When I google I get some of the old emails on g_msd from the gromacs website, but I can only read some of them (the others direct me to an empty page in the new webpage). 


The first question is whether I can use my .xtc file made with this command from the original .trr file:

trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s dmpclim32-1.tpr -o dmpclim32-all.xtc  (for fitting and centring the DMPC group is used)

I would guess I could not, but should I then do the command again creating a new .xtc file, but without using -center and -pbc whole?


My second question is why g_msd has the option -rmcomm to remove COM motion? How is g_msd created so that the diffusion coefficient can be calculated if COM motion is removed?


Thank you very much for your time,


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