normal Proper dihedrals

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7 years 5 months ago #5923 by nilusha
Proper dihedrals was created by nilusha
Hi,

I was trying to add proper dihedral potentials to the backbone dihedral angles of a LYS chain.I created the topology file for the LYS chain using the martinize V:2.4 script (coil secondary structure)and added the proper dihedrals manually in order to reproduce the all atom dihedral distribution. I did the minimization and and then tried the equilibration. I got a segmentation error during the equilibration. My force constant = 7.5, angle = 0 and multiplicity= 1, time step= 20fs. Do you suggest any reason for this?

Thank you!!

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7 years 5 months ago #5925 by flaviyan
Replied by flaviyan on topic Proper dihedrals
which four Beads did you take into account for the dihedral ? martini lysine only has 3 beads (BB-SC1-SC2) and there is already an angle parameter for these three beads.

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7 years 5 months ago #5926 by peterkroon
Replied by peterkroon on topic Proper dihedrals
Which version of Martini did you use? Are you sure the parameters you put into martinize are propagated to your itp file? Are you doing NPT or NVT equilibration?

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7 years 5 months ago - 7 years 5 months ago #5928 by nilusha
Replied by nilusha on topic Proper dihedrals
Hi,

My system has 20 LYS amino acids. I have defined dihedral angle using four backbone beads (BB-BB-BB-BB). So there are 17 dihedral angles for 20 LYS.
This is how I defined it.

[dihedral]
1 4 7 10 1 0.0 7.5 1
.........

I use Martini 2.1 version and I am doing NPT equilibration.

Thank you!
Last edit: 7 years 5 months ago by nilusha.

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7 years 5 months ago #5929 by peterkroon
Replied by peterkroon on topic Proper dihedrals
Does the simulation work without your dihedrals (same input structure)?
Otherwise I *think* it's most probable one of your dihedrals is adopting a (near) linear conformation, in which case the maths blow up (i.e. the four backbone beads are on a straight line).

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7 years 5 months ago - 7 years 5 months ago #5930 by nilusha
Replied by nilusha on topic Proper dihedrals
Yes, Simulation worked well without dihedrals.
Also the equilibration worked with dihedrals when I reduced the force constant to 3.5 instead of 7.5. However the production run didn't work with 3.5 force constant.

Yes, That might be a reason. Do you have any suggestions that I could try?
Thank you!
Last edit: 7 years 5 months ago by nilusha.

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7 years 5 months ago - 7 years 5 months ago #5958 by peterkroon
Replied by peterkroon on topic Proper dihedrals
I seem to remember there was a workaround for this, I just can't recall what is was exactly :(
IIRC one option is to use angle constraints of sorts, I can't find the reference for this, but I'll ask around (but don't get your hopes up)

I'll also ask around for other options...

Edit: Apparently the answer is "Restricted bending angles" (or something) in Gromacs 5. Also read DOI 10.1063/1.4937783 for an example (the bacteriohopanetetrol tail).
Last edit: 7 years 5 months ago by peterkroon.

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