normal lipid bilayer minimization

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10 years 3 months ago #3113 by ipsita
lipid bilayer minimization was created by ipsita
Sir,
I'm a beginner in coarse graining and also in gromacs. I've an all atom lipid bilayer structure which I converted to a CG model using MARTINI. Now when I start the minimization process with the em.mdp file supplied in your tutorial, the bilayer structure is just reversed i.e
tail-head-water-head-tail instead of
water-head-tail-tail-head-water.
When I turn off pbc , then the structure is okay.
So what should I do or change in the mdp file to ix the problem?
Please help.

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10 years 3 months ago #3114 by xavier
Replied by xavier on topic lipid bilayer minimization
From what you describe it does not seem that the inversion you describe is real. It is a simple effect of pbc.

If you translate your system by a few nm in the right direction you'll replace the position of the box in respect to the center of the bilayer and thus the bilayer would not be separate the same day.

trjconv and editconv may help you play with this translation.

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10 years 3 months ago #3215 by ipsita
Replied by ipsita on topic lipid bilayer minimization
Sir, I checked the coordinate of the center of mass, it is 0.0025 -0.0001 0.0073. So why should I translate the system? And still the problem is same. It is okay without pbc. What should I do?

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10 years 3 months ago - 10 years 3 months ago #3217 by Clement
Replied by Clement on topic lipid bilayer minimization
It's not a simulation problem. It's a visualization issue. Think Periodic Boundary Images, switch some images on in VMD for instance if you need to visualize it: your system is still the same.

The system translated along the z-axis (if z is the axis parallel to the normal to the bilayer plane) during the simulation; but according to the PBC, it doesn't change anything (that's what PBC means). Try re-centering your system (trjconv -f <XTC> -s <TPR> -center; two questions asked when running this command line: which index to use to recenter [in your case your bilayer] and which index to output [in your case the system or whatever you're interested in]), as Xavier just mentioned above.

Turning off PBC will just lead to unrealistic simulations. And the effective center of mass of your bilayer will no change of course, since in your system lipids are on each side of the box...
Last edit: 10 years 3 months ago by Clement.

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10 years 3 months ago #3218 by ipsita
Replied by ipsita on topic lipid bilayer minimization
Thank you very much. Your suggestion really helps. Now after translating and centering the structure is perfect after minimization. Now When I started to run the system with position restrained, the job is aborted after 500ps giving Lincs error. Except the timestep (10fs) and the temperature (300K)all parameters are unchanged in the supplied md.mdp file. But the structure in vmd is okay. Is it an initial problem, should I restart from the end point?

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10 years 3 months ago #3219 by Clement
Replied by Clement on topic lipid bilayer minimization
Are you simulating only lipids? What kind of lipids?

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10 years 3 months ago #3226 by ipsita
Replied by ipsita on topic lipid bilayer minimization
Yes, I've only lipids in my system. The lipids are phospholipids and cholesterol.

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10 years 2 months ago #3379 by ipsita
Replied by ipsita on topic lipid bilayer minimization
If I set the timestep lower than 10fs, then the simulation run without giving any error, but if I tried ti increase the timestep to 10fs or more than that, then after few ps, it gives lincs error and then aborted. I checked the structure in vmd, all are okay. PLease help.

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10 years 2 months ago #3382 by Clement
Replied by Clement on topic lipid bilayer minimization
All isn't OK if it crashes... Probably a cholesterol going crazy, the current structure available on the website is kinda under tension. We're fixing that.

But it SHOULD run at 10 fs without problems. You can tune the LINCS behavior in your .mdp file. Try to increase the order of the constraint matrix for instance, or the number of iterations. The keywords below:

; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30

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