GROMACS version:
GROMACS modification: Yes/No
Here post your question
Hello everyone,
I am trying to calculate viscosity of a cluster of proteins in solution. I have set up the system using MARTINI 2.2 force field in GROMACS 5.1.5. I want to proceed by first finding the position dependent diffusion coefficient.
Can someone help me with the steps I need to follow in order to find the diffusion coefficient? I started with gmx msd but I am not sure if I am correct. Thank You.
gmx msd -seltype mol-com should get you the diffusion coefficient.
Thank you for replying. However, I could not figure out what is -seltype? It shows invalid command.
I am trying with the following command -
gmx msd -f final.xtc -s *.gro -n *.ndx -type x -mol com -o test_diff.xvg
and I am getting the error message -
Fatal error:
Could not read a topology from prod_3.part0003.gro. Try a tpr file instead.
I could not use the *tpr file instead as I generated it on a cluster and the file is incompatible with my computer system. Can you please suggest something regarding this? Thank you.
tpr files are compatible across all systems, unless you created it with a newer version of GROMACS than on your computer system. In that case I would suggest to simply recreate the tpr.
Yes, the tpr file generated was on a newer version of GROMACS.