GROMACS version: 2020.6
GROMACS modification: No
Dear GMX users,
I would like to analysis MSD analysis for a small molecule in a solution. Simulation is 600 ns long.
I run following command:
gmx msd -f …/md1.xtc -s …/md1.tpr -mol diff.xvg -o msd_md1.xvg
However, it responses killed as following:
Split group of 147 atoms into 1 molecules
Last frame 24000 time 600000.000
Used 12001 restart points spaced 10 ps over 600000 ps
Killed
If you have any experience, please give me some advice.
Best regards,
Mijiddorj
I had the same problem before, I believe you’re running out of memory, as the msd algorithm tends to use excessive amounts of memory - a problem that’s been around, and discussed in the mailing list for some time - you can check by putting your command into the background and then look at memory usage with the ps or free unix commands.
A workaround is to split the total MSD into roto-vibrational and translational parts, but that’s rather cumbersome … you transform your trajectory into another trajectory containing only the center of mass of your molecule(s), and make a pseudo topology and tpr file for that one atom molecule and then calulate the msd for that which gives you the translational part. then you’s convert the trajectory of individual molecules so that their individual COMs are shifted to the origin, from this directory you can calculate the roto-vibrational part of the MSD, this second part you’d have to do for each of your solvent molecules separately.
good luck,
mic