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minimization-vac.mdp
- imankatouzian
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4 years 2 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,
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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- riccardo
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4 years 2 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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- brajk
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3 years 7 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!
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
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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- vainikka
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3 years 7 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.
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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- brajk
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3 years 7 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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