I am trying to simulation protein in non-aqueous solvents and I put my protein in MeOH with Charmm36 force field. After I tried to minimize the energy. it gives:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step.
Steepest Descents converged to machine precision in 1380 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -5.0106647e+05
Maximum force = 8.7402100e+03 on atom 26862
Norm of force = 9.7398650e+01
I first thought the protein might not be stable in MeOH. Then I tried to solvate the protein in water and add few MeOH melocules (3 molecules). However, after minimization I have the same problem.
Can anyone help with this please?
Thank you!
Hey Yang! What you call as a problem is not a problem in reality. You perform the energy minimization in order to prepare your system for equilibration and then production runs, for example, if you created the system with many overlaps of molecules the energy minimization will take away those overlaps. What you got is not an error message, it was a report that there was no difference between energies during 2 steps. You shall start doing equilibration then by using other advanced algorithms for temperature and pressure coupling. For those steps you shall use the resulting file confout.gro after that energy minimization. Nevertheless, if you wish to do more energy minimizations to your systems you can, for example, vary the step-size and the tolerance in your mdp-file. You may switch "the integrator" from steep to cg or vice versa. You shall be concerned about your simulation only if you get error messages, when mdrun does not produce any gro-files or it will produce a huge number of step*.pdb-files.
you chance number of cycles of minimization (50,000) of emtol option to 10000 or use restraint to solute and following cycle without restraint to solute, for get correct minimization of system, use isotropic harmonic restrainst, with the command gmx genrest of groma, before create index for only solute add this to topol.top and add a mdp file de minimization Define flag.
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