Grace Tang wrote:
Hello All,
I am doing energy minimization on a protein crystal structure to relax
it. Afterwards, I plan to run md simulation with implicit solvent. I
am new at this and have many questions.
1. Should the implicit solvent conditions be enabled when I run the
energy minimization?
No - while GROMACS has some vestiges in the user interface of an earlier
attempt to implement implicit solvation simulations, these will not
functional until at least version 4.1.
2. What minimum potential energy should I expect (i know that when
explicit water is present, the energy often reaches -10E5 or -10E6)
Negative, and vaguely proportional to the number of atoms.
3. What kind of emtol is appropriate? Is it better to set it high so
that the system converges, or is it okay if machine precision is reached.
It's pretty much irrelevant for preparing a system for MD. You'll have
to equilibrate it later, and the value of an EM step is merely relieving
any bad atom-atom contacts before they turn into huge accelerations. If
the equilibration doesn't crash, you did enough EM.
Mark
Below are 2 example runs I did with implicit_solvent = no
When I decreased the step size, the system did not converge anymore. I
was wondering if this was due to chance, precision issues (I am using
single precision), or perhaps the emstep = 0.1 was reaching a nearby
minimum and 0.01 was reaching the local minimum. Note, maximum force
gets rather large when convergence is to machine precision.
emtol = 1000
emstep = 0.1
Steepest Descents converged to Fmax < 1000 in 29 steps
Potential Energy = -4.9613008e+003
Maximum force = 6.4596338e+002 on atom 235
Norm of force = 1.0625026e+002
emtol = 1000
emstep = 0.01
Steepest Descents converged to machine precision in 25 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -3.9642480e+003
Maximum force = 5.1200122e+003 on atom 416
Norm of force = 3.6602789e+002
Any advice is greatly appreciated. Much thanks!
- Grace
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