[gmx-users] Implicit Solvent System - Energy Minimization
gwtang at stanford.edu
Wed Apr 15 19:26:10 CEST 2009
Sorry, I wasn't too clear in the first message. I will be using OpenMM
Gromacs, which does support implicit solvent. My current energy
minimization steps only lower the energy to -5E3. Is this okay considering
water is not around?
Is is necessary to do equilibration if I am using implicit solvent? Is so,
can anyone direct me to reasonable parameters?
On Wed, Apr 15, 2009 at 2:55 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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
> 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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