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Dry Martini Tutorial
- jcantero
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8 years 9 months ago #4691
by jcantero
Dry Martini Tutorial was created by jcantero
I'm trying to use the new Dry Martini, and using the tutorial for the first time.
I create the vesicle with the vesicle builder script
It creates the vesicle, with the cholesterol right in the middle of the bilayer. in the image, in yellow are PO4 and C3A beads, cyan and purple is cholesterol.
This image is hidden for guests.
So, for minimization, since Dry Martini requires specific parameters, I only changed the integrator to steep and left everything else intact. Yet, it couldn't minimize the system.
I've worked with cholesterol in classic Martini, so I don't think it's the virtual sites or constraints. If there were differences in bead numbers, it would have showed up when using grompp. So, maybe it's the position of the cholesterol between leaflets that's causing the problem?
And then, I create a DPPC:DUPC 60:40 vesicle without cholesterol, and there wasn't any problems minimizing it. (i'm using Gromacs 4.6.6 in Ubuntu 14.04.02 LTS by the way)
Has anyone encounter this problem? Is it just me? Am I missing something?
Thanks in advance,
Jorge
I create the vesicle with the vesicle builder script
martini_vesicle_builder.py 12.5 DPPC:DUPC,60:40 43 1> system.gro 2> system.top
It creates the vesicle, with the cholesterol right in the middle of the bilayer. in the image, in yellow are PO4 and C3A beads, cyan and purple is cholesterol.
This image is hidden for guests.
Please log in or register to see it.
So, for minimization, since Dry Martini requires specific parameters, I only changed the integrator to steep and left everything else intact. Yet, it couldn't minimize the system.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = 9.0731605e+16
Maximum force = inf on atom 13308
Norm of force = inf
I've worked with cholesterol in classic Martini, so I don't think it's the virtual sites or constraints. If there were differences in bead numbers, it would have showed up when using grompp. So, maybe it's the position of the cholesterol between leaflets that's causing the problem?
And then, I create a DPPC:DUPC 60:40 vesicle without cholesterol, and there wasn't any problems minimizing it. (i'm using Gromacs 4.6.6 in Ubuntu 14.04.02 LTS by the way)
Has anyone encounter this problem? Is it just me? Am I missing something?
Thanks in advance,
Jorge
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- helgi
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8 years 9 months ago #4723
by helgi
Replied by helgi on topic Dry Martini Tutorial
Hello, hello,
You are right it is not the number of beads as that would show up in grompp. But you should try the cholesterol without constraints – for the minimization then switch back after minimization. The problem is that with constraints the energy can get really large with only small deviations in structure so if the initial structure is not exact you need to use the non-constraint cholesterol. Also in insane there is random rotation and sometimes these will results in too close beads or lead to non-ideal structures so you can re-run insane with a different “–rand” flag.
hope this helps,
cheers,
- Helgi
You are right it is not the number of beads as that would show up in grompp. But you should try the cholesterol without constraints – for the minimization then switch back after minimization. The problem is that with constraints the energy can get really large with only small deviations in structure so if the initial structure is not exact you need to use the non-constraint cholesterol. Also in insane there is random rotation and sometimes these will results in too close beads or lead to non-ideal structures so you can re-run insane with a different “–rand” flag.
hope this helps,
cheers,
- Helgi
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