normal Martini parameters for RNA

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2 years 10 months ago #5566 by bt12d026
Martini parameters for RNA was created by bt12d026
Hi,
I would like to simulate protein-RNA complex. When can we expect the avaialability of Martini parameters for RNA?

Thank you

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2 years 10 months ago #5567 by jaakko
Replied by jaakko on topic Martini parameters for RNA
Hi,

This should be possible soon! I expect we will put the beta parameters out within a month and submit the paper soon after that. If you're in a hurry I can send the RNA parameters (only with a stiff elastic network currently).

- Jaakko

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2 years 10 months ago #5569 by bt12d026
Replied by bt12d026 on topic Martini parameters for RNA
Hi Jaakko,
Thank you for the quick reply. Actually, we are in hurry to wind-up the work. So, Can you please send me the RNA parameters off-list? I will also use the beta version of the RNA parameters as soon as they are uploaded. Thank you for the help.

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2 years 10 months ago #5572 by jaakko
Replied by jaakko on topic Martini parameters for RNA
Sure, email me at This email address is being protected from spambots. You need JavaScript enabled to view it. and I'll send you the parameters (I expect the beta to be identical to this).

- Jaakko

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2 years 9 months ago #5604 by bt12d026
Replied by bt12d026 on topic Martini parameters for RNA
Hi Jaakko,
I tried to perform CG simulations using the beta version of the RNA parameters. I have well equilibrated my system by performing approximately 1 microsecond gas-phase AA-simulation. But the CG-smilutaion on this gas phase equilibrated structure is terminating with LINCS warnings. I changed integration step, but still no profit. Is there something I overlooked? I am using gromacs-5.1.2 version. The mdp parameters I considered are listed below. Thank you for your time and concern.

integrator = md
dt = 0.01
nsteps = 1000000
nstxout = 0
nstvout = 0
nstlog = 1000
nstxtcout = 1000
xtc-precision = 10
rlist = 1.4
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15
rvdw = 1.1
tcoupl = berendsen ;v-rescale
tc-grps = System
tau_t = 2.0 ;0.5
ref_t = 310
Pcoupltype = isotropic
Pcoupl = berendsen ;parrinello-rahman
tau_p = 4.0 ;4.0
compressibility = 3e-4 ;4.5e-5
ref_p = 1.0
gen_vel = no
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005

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2 years 9 months ago #5605 by jaakko
Replied by jaakko on topic Martini parameters for RNA
Hi,

what type of RNA structure are you trying to simulate? Just to check, do you have a solvent in the CG simulation or is that in gas phase as well?

I haven't tested the RNA model at all with the verlet cut-off scheme so that could be an issue but otherwise the parameters look fine. I'd recommend you try running the system using the example mdp that comes with the DNA package just to see if the problem is in the parameters.

- Jaakko

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2 years 9 months ago #5608 by bt12d026
Replied by bt12d026 on topic Martini parameters for RNA
Hi,
I am trying to simulate ss-RNA with stiff elastic parameters. There is no solvent currently. I am trying to relax RNA under gas-phase. I have changed the cut-off scheme to Verlet inorder to simulate using Gromacs-5.1.2. Anyway I will try to simulate using Gromacs-4.5.7 and will update the status.

Thank you

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2 years 9 months ago #5614 by jaakko
Replied by jaakko on topic Martini parameters for RNA
Hi,

Martini really isn't parameterized for gas phase so I wouldn't recommend using it for that. Also note that the stiff elastic network is actually stiff and your structure won't change much in simulation.

- Jaakko

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2 years 2 months ago #6856 by bt12d026
Replied by bt12d026 on topic Martini parameters for RNA
Hi Jaakko,
I am trying to perform Protein-RNA complex simulation using example.mdp parameters provided in the DNA tutorial. I have thoroughly equilibrated the system with dt = 2fs and subsequently with dt= 5fs. However, when I try to perform the simulation with either dt=20fs or dt=10fs, the system is unstable and giving LINCS warnings. Kindly suggest some solution.

Thank you

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1 year 10 months ago #7258 by spirhadi
Replied by spirhadi on topic Martini parameters for RNA
Hi there,

I am trying to parametrize a double strand RNA with martini coarse grain force field. Is there any python file or something available for doing this. Any help is greatly appreciated.

Bests,
Somayeh

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1 year 10 months ago #7271 by ifaustino
Replied by ifaustino on topic Martini parameters for RNA
Hi,

We have just uploaded the beta version of the Martini RNA parameters in the Downloads section of the cgmartini website. The tar file contains the martinize script for both DNA and RNA molecules together with the backmapping files to convert from coarse grain to all-atom resolutions. The usage and analysis is similar to the DNA process explained in the DNA tutorial.

If you have any questions, please use the Martini forum. Thanks.

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