[gmx-users] Implicit Solvent System - Energy Minimization
Mark.Abraham at anu.edu.au
Wed Apr 15 11:55:26 CEST 2009
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.
> 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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