Energy minimzation

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1

Dear all,

I’m trying to add hydrogen atoms to a protein structure and perform energy minimization in a solvated system with ions. However, I’m encountering an issue where one hydrogen ends up too close to a non-bonded oxygen atom (see attached figure). The oxygen is part of a group that I need to keep completely fixed.

I’ve tried several minimization settings, including:

  • integrator = steep and cg
  • emtol = 1000, 100, and 10
  • emstep = 0.01 and 0.02

Unfortunately, none of these changes resolved the clash.

Below is the .mdp file I’m using. I would really appreciate any suggestions or ideas for how to address this while keeping all heavy atoms fixed.

ini

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; Minimization parameters
title           = Minimization

; Freeze heavy atoms
freezegrps      = Protein-H
freezedim       = Y Y Y

; Minimization settings
integrator      = steep       ; (also tried cg)
emtol           = 1000.0      ; (also tried 100 and 10)
emstep          = 0.01        ; (also tried 0.02)
nsteps          = 50000

; Neighbor search and interactions
nstlist         = 1
cutoff-scheme   = Verlet
ns_type         = grid
rlist           = 1.2
coulombtype     = PME
rcoulomb        = 1.2
vdwtype         = cutoff
vdw-modifier    = force-switch
rvdw-switch     = 1.0
rvdw            = 1.2
pbc             = xyz
DispCorr        = no

Thanks in advance for your help!

Best regards,
Miriam

image
image1239×796 74.5 KB

2

Have you tried a (much) smaller emstep, e.g. 0.001?