I have energy minimized my structure using gromacs for 20 ps following the lysozyme tutorial.
I did 3 such replicates for the minimization. The potential energy for all these 3 replicates was the same and there were no differences in the log files except the id.seed values.
I am confused as if energy minimization is a stochastic process Shouldn't there be some difference in the values??
Hello,
No, the potential energy depends upon the ligand bound in the active site of the receptor. But, the conformations of amino acids change with each experiment so the potential could be changed quitely.
No, Because every replica has a different temperature. It will not be the same. In REMD the distribution of PE will not be the same.
Most likely yes.
The energy minimization is not a normal "dynamic" simulations, like NVT, NPT etc. Your results depend on the algorithm you are using for minimising the system. If you are using the normal EM procedure in GROMACS (integrator=steep ) then you are using a steepest descent method which is based on gradient calculations for minimising the configuration by moving atoms that have very high forces between them. The algorithm, ideally, should be deterministic, that is, if you start from the same identical structure and you use the same parameters in the .mdp file (emtol, emstep, constraints etc) then yes, you will most likely get the same identical results. In a way, you are calculating numerical derivatives three times for the same systems with the same coordinates: you SHOULD get the same results.
if you are talking about individual 3 sets of the same system. The energy should be the same. But in the case of REMD, it will not be.
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