GROMACS version: 2022
Dear Gromacs users,
I am studying the diffusion of water in MFI zeolite. The simulation is done without any errors. However, When I want to calculate the diffusion coefficient of water using gmx msd I see this message on the terminal screen:
there were 2136 inconsistent shifts. check your topology.
The Structure is periodic and I have applied PBC in three directions. I get a linear MSD and diffusion coefficient as output. However, my concern is that this diffusion coefficient is not reliable. What is the problem? Is there any consideration for such systems? I also added periodic-molecule = yes to the .mdp file. But still, the inconsistent shift exists.
Thanks for your help
Have you corrected the PBC effects in your trajectory before performing the analysis? If not, you need to remove any jumps across the simulation box. To achieve this, you can use the trjconv utility in GROMACS. Refer to the following link for further guidance: https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow
Can you suggest a way in which I can generate topology files for protein with GDP in it?
The "2136 inconsistent shifts" message in GROMACS suggests problems with periodic boundary conditions or topology. Even though you added periodic-molecule = yes, the issue may still arise from an improperly defined topology or insufficient box size, which causes molecules to shift incorrectly across boundaries. Double-check your topology and ensure the simulation box is large enough to prevent overlaps.
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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