After about 600ns of my MD run, I notice that my molecule has started interacting with the image. I understand that I should use a larger box length but is it possible for me to continue the MD from this point onward some how or should I start my MD run from the beginning with a larger box dimension?
I am using GROMACS 18.3 and simulating a large protein-nucleic acid complex.
You cannot extend it with different box dimension since you need to use 'gmx solvate' again to specify the box size instead of using files from your last production run
You have to define the box with larger dimension, and starts simulation from the beginning. In this case you can n't extend box dimension by using extend and append gmx tool command ,because they are only valid for extend time of simulation not for editing periodic boundary condition.
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