Dear All,
I have come across something strange while doing RMSD calculation.
I calculated the RMSD of a mutated protein using the .tpr file generated from Wild type and it does the calculation without any error. Both the systems have different number of atoms and I was anticipating an error, but that didnt happen. Infact, I tried the calculation using totally unrelated .tpr from a different protein and yet it prints some values.
Now I'm totally confused about whats happening. I tried the calculation using two versions of gromacs:2020.2 and 2022 as well.
Can anyone explain what might have gone wrong here ? Or am I making some mistake in understanding.
Thanks and Regards
Kindly check the contents of both the tpr files using the 'gmx check' function. Maybe the mutation is not applied correctly in the WT.
RMSD calculation in GROMACS compares atom positions between frames, not atom types. If the atoms in the different proteins have matching atom indices, it might still calculate RMSD, despite differences in structure. Ensure you are comparing the correct atom selections, and check the topology files to avoid mismatches.
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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