GROMACS version: 2021
GROMACS modification: No
Dears Gromacs users,
I’m a new user so I have some doubts about the MD parameters.
I performed an MDS on a large protein (about 1200 residues) following the lysozyme tutorial.
My simulation was time- and computational-expansive.
Any suggestion to optimize the parameters?
How long does it take for a simulation of this type with a standard laptop?
Thanks in advance.
The size of your protein in terms of amino acids is not terribly informative; its geometry is as it dictates the requisite size of the box, which will then determine the number of waters and how many total atoms you will have. This is the biggest determining factor for the performance of the simulation.
What parameters? Most of the input parameters in terms of nonbonded settings are baked into the individual force fields and shouldn’t be adjusted, otherwise you’ll invalidate (or put into serious question) the physical model.
I don’t know what qualifies as a “standard” laptop these days, but it is generally inadvisable to try to run MD on one. Laptops aren’t cooled sufficiently well for computationally intensive processes like MD.