normal Energy minimization of complex membrane

  • bbm
  • bbm's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 months 3 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.

Please Log in or Create an account to join the conversation.

More
9 months 1 week ago #9654 by vainikka
Replied by vainikka on topic Energy minimization of complex membrane
Hi,

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

Please Log in or Create an account to join the conversation.

Time to create page: 0.164 seconds