GROMACS version: 2020.4
GROMACS modification: No
Dear all,
I have successfully used the cluster tool to obtain different conformations of a simple solute+solvent system, previously obtained with the REMD methodology.
The problem occurs when running a simulation starting from a structure obtained with the cluster. With the cluster tool, I get different configurations of the solute, and from these configurations, I start a new simulation. During energy minimization, errors such as:
##################
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 0.01.
Potential Energy = 3.7985155e+16
Maximum force = inf on atom 682
Norm of force = inf
############
This problem occurs in all configurations that I submit to a new simulation.
The solution that I am using is to increase the size of the simulation box, centralizing the configuration obtained via cluster and filling the empty space with the same solvent. The central portion of the new simulation box is similar to the configuration obtained with the cluster. It doesn’t make sense to me that I can’t perform an energy minimization on any frame of the simulation.
Does anyone have any idea how to work around this problem without having to modify the simulation box?
best