normal minimization-vac.mdp

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4 years 4 months ago #8424 by imankatouzian
minimization-vac.mdp was created by imankatouzian
Good day,

I am new to the martini simulation and am practicing tutorials right now. I have all the .mdp files however about the minimization-vac.mdp I got errors since I have modified the martini_v2.x_new-rf.mdp from website and cannot make it myself according to the tutorial text file as it says :
[ get martini_v2.x_new-rf.mdp from website, Aug 03 2017, make a copy and change settings for minimization and later on for equilibration and production (dynamic) ]
can sb help me with this or send me the
minimization-vac.mdp file so that I can use it in my simulations.
Thanks.

Best,

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4 years 4 months ago #8427 by riccardo
Replied by riccardo on topic minimization-vac.mdp
You can find examples of minimization in vacuum for example in this tutorial www.cgmartini.nl/index.php/tutorials-gen...ng-new-molecule-gmx5 (specifically, at www.cgmartini.nl/images/stories/tutorial...ion/minimization.mdp ).

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3 years 9 months ago #8719 by brajk
Replied by brajk on topic minimization-vac.mdp
Hi there,

I'm new to the field of coarse-grained simulations of protein-membrane interactions. I've used insane.py to create a lipid bilayer with thylakoid lipids (15 % OPSG, 13 % OPPG, 54 % OPMG, 18 % OPGG). Then, I've tried to energy minimize the lipid bilayer using adapted .mdp options from www.cgmartini.nl/images/stories/tutorial...ion/minimization.mdp

However, the system doesn't minimize and I get the following message:

Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 10.
Potential Energy = 1.7086083e+17
Maximum force = inf on atom 17112
Norm of force = inf

I've tried to work with a smaller patch (-x 10 -y 10 -z 10) and the minimization worked. Which .mdp options should I optimize/change such that the minimization works for a larger patch?

Thanks a lot!
integrator               = steep
dt 			 = 0.02
nsteps                   = 1000
nstxout                  = 0
nstfout                  = 0
nstlog                   = 100 

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

coulombtype              = PME
rcoulomb                 = 1.1
epsilon_r                = 2.5    
epsilon_rf               = 0
vdw_type                 = cutoff  
vdw-modifier             = Potential-shift-verlet
rvdw                     = 1.1

command for insane.py:
insane.py -o bilayer.gro -p bilayer.itp -pbc cubic -x 20 -y 20 -z 20 -l OPSG:15 -u OPSG:15 -l OPPG:13 -u OPPG:13 -l OPMG:54 -u OPMG:54 -l OPGG:18 -u OPGG:18 -sol PW:10 -salt 0.15 -charge -376

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3 years 9 months ago #8720 by vainikka
Replied by vainikka on topic minimization-vac.mdp
Hi,

The energies and forces you get out after minimization indicate that two or more beads are overlapping. Just run insane again and generate a new starting configuration.

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3 years 9 months ago #8721 by brajk
Replied by brajk on topic minimization-vac.mdp
Thank you very much for the quick response!

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