[gmx-users] Implicit Solvent System - Energy Minimization
gwtang at stanford.edu
Wed Apr 15 09:21:45 CEST 2009
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
2. What minimum potential energy should I expect (i know that when explicit
water is present, the energy often reaches -10E5 or -10E6)
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.
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!
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