normal Energy minimization of complex membrane

  • bbm
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1 year 2 weeks ago #9642 by bbm
Dear martini users,

I am currently working on a complex membrane simulation using martini forcefield. 6 different lipid molecules in various proportions are present. I have prepared the system using charmm-gui martini maker. I am using polarizable martini water molecule. The energy minimization step is not working well. I am using the following mdp parameters:
integrator = steep
emtol = 100
nsteps = 10000
nstxout = 0
nstfout = 0
nstlog = 100

cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 2.5 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

Fmax is not converging below 100 kJ mol-1 nm-1, and the Fmax is almost 800-850 kJ mol-1 nm-1 much further away from Fmax. Also when I visualize the gro file generated after the energy minimization step, that looks very different, weird gaps are formed between water molecules, like they are forming clusters. I have checked the file before energy minimization, things look fine. Can anyone suggest any workaround? Any help will be much appreciated.

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11 months 4 weeks ago #9654 by vainikka
Replied by vainikka on topic Energy minimization of complex membrane

I tested a Martini 2.2P system with a mixed lipid bilayer, and constraints for the PW - no issues that I could spot.

You mentioned that you've built the system using CHARMM-GUI, yet the .mdp options you copied here do not include the soft-core minimization parameters which CHARMM-GUI mdps have on their first minimization step. Are you using the .mdp files provided by CHARMM-GUI? If not, I'd suggest you do - the first step (step6.0), which uses the soft-core potentials, can be useful if the starting configuration has a lot of clashes.

In case you don't have the .mdp files, you can paste these to the minimization .mdp file you're currently using:

; Free energy parameters
free-energy = yes
init-lambda = 0.01
sc-alpha = 4
sc-power = 2
sc-coul = yes
nstdhdl = 0
couple-moltype = system
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw-q
; in the final state, both are off.
couple-lambda1 = none
couple-intramol = yes
refcoord_scaling = all

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