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bond breaking of cholesterol
- ipsita
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10 years 2 months ago #3495
by ipsita
bond breaking of cholesterol was created by ipsita
Sir, I have a bilayer system containing POPC and CHOLESTEROL. For mdrun, I use timestep as 10fs. When I visualise the trajectory in vmd, some bond breaking in cholesterol is observed, but when I look at the final output gro file, it is perfectly okay. So is there really anything wrong in my system or what may be the issue? Please help.
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- Clement
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10 years 2 months ago #3496
by Clement
Replied by Clement on topic bond breaking of cholesterol
Mmmmh... We're going to need more input here. What do you mean by "breaking"? Deformation? Do you get any error?
Remember that visualization can be tricky with CG models...
Remember that visualization can be tricky with CG models...
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- ipsita
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10 years 2 months ago #3497
by ipsita
Replied by ipsita on topic bond breaking of cholesterol
bond breaking I visualise some CG beads of one or two cholesterl is going far apart from another part while the other cholesterols are okay. And no, I don't get any error. The simulation is running smoothly without giving error.
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- ipsita
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10 years 2 months ago #3499
by ipsita
Replied by ipsita on topic bond breaking of cholesterol
Should I need to modify the itp for cholesterol or it is a visualization issue? PLease help.
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10 years 2 months ago #3500
by Clement
Replied by Clement on topic bond breaking of cholesterol
If you don't have any error, I'd say it's a visualization issue... Can't really say more with what you're describing.
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- ipsita
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10 years 2 months ago #3503
by ipsita
Replied by ipsita on topic bond breaking of cholesterol
Sir, even I reduce the time step to 4fs, the system run a few micrsecond without any error and the final gro file is okay. But if i look the trajectory in vmd, it shows that some cholesterols are not intact, they are breaking. I really can't understand should I proceed or not as I am a beginner in martini cg. I'm confused that it is a visualization problem or not. I downloaded cg_bonds.tcl, but before reading the trajectory when I run the cg_bonds -molecule "top" command,it shows can't read "molecules":no such variable. So please help to proceed further.
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- xavier
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10 years 2 months ago #3504
by xavier
Replied by xavier on topic bond breaking of cholesterol
Your simulation is perfectly fine and you do not need to decrease your time step! 20/40 fs should be fine as long as you do not get an error message while running the md code.
Prior to visualisation with vmd you need to rebuild the molecule whole using a gromacs tool. It would go like this:
trajconv -f mytraj.xtc -s mytpr.tpr -pbc mol -o mytraj-mol.xtc
the option "-pbc mol" will force the program to write molecule whole instead of breaking them at the boundary of your box. You need to give a tpr file for the system to know what is a molecule.
Prior to visualisation with vmd you need to rebuild the molecule whole using a gromacs tool. It would go like this:
trajconv -f mytraj.xtc -s mytpr.tpr -pbc mol -o mytraj-mol.xtc
the option "-pbc mol" will force the program to write molecule whole instead of breaking them at the boundary of your box. You need to give a tpr file for the system to know what is a molecule.
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- ipsita
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10 years 2 months ago #3505
by ipsita
Replied by ipsita on topic bond breaking of cholesterol
Thanks a lot. It really helps. I just needed this. After making axtc file like this, I found no breaking during visualization.
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10 years 2 months ago #3506
by ipsita
Replied by ipsita on topic bond breaking of cholesterol
If I add GM1 in my system, then if I use timestep as 10fs, the mdrun abrots after 5-6ns giving LIncs warning. Should I reduce the timestep if I use GM1 in my system?
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10 years 2 months ago #3507
by Clement
Replied by Clement on topic bond breaking of cholesterol
I seem to remember GM1 forces a timestep of 5fs... But I might be wrong.
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10 years 2 months ago #3508
by siewert
Replied by siewert on topic bond breaking of cholesterol
Please read the paper describing the glycolipid parameters:
C.A. Lopez, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids. JCTC, 9:1694–1708, 2013
Here the limitations of the GM1 parameters and timesteps are clearly explained.
C.A. Lopez, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids. JCTC, 9:1694–1708, 2013
Here the limitations of the GM1 parameters and timesteps are clearly explained.
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