[gmx-users] Implicit Solvent System - Energy Minimization

[Mark Abraham]

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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