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angle parameter in cg topology
- msaeedi
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10 years 7 months ago #1859
by msaeedi
angle parameter in cg topology was created by msaeedi
Hi,
i had a AA simulation and determine distance for center of mass two groups with g_dist.
i put them in cg topology.i want to determine angle parameter for beads.but i dont know what can i do?
how can measure angle for center of mass 3 groups from atomistic simulation?
i searched in gromacs searching mail and found g_angle -ov .is it correct to use this?
thanks
i had a AA simulation and determine distance for center of mass two groups with g_dist.
i put them in cg topology.i want to determine angle parameter for beads.but i dont know what can i do?
how can measure angle for center of mass 3 groups from atomistic simulation?
i searched in gromacs searching mail and found g_angle -ov .is it correct to use this?
thanks
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- Clement
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10 years 7 months ago - 10 years 7 months ago #1863
by Clement
Replied by Clement on topic angle parameter in cg topology
g_angle is what you need to use to extract angles. The output given by the -ov flag is not what I'd use though: it gives you only the average angle, and doesn't give you information about a potential multiple components distribution (multiple preferential orientations). You should use the -od flag, which gives you the complete distribution; you can then adapt the value(s) for you angle(s).
Another thing: g_angle can be used for angle AND dihedrals.
Another thing: g_angle can be used for angle AND dihedrals.
Last edit: 10 years 7 months ago by Clement.
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- msaeedi
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10 years 7 months ago - 10 years 7 months ago #1864
by msaeedi
Replied by msaeedi on topic angle parameter in cg topology
Thanks for your reply.
I used:
g_angle -f md.xtc -n index.ndx -od dist.xvg,index.ndx file are consist of all atoms in 3 beads.
but in dist.xv file,there ware two peaks,in other words,i had two angle that have most distribution.
which angle should i use?
I used:
g_angle -f md.xtc -n index.ndx -od dist.xvg,index.ndx file are consist of all atoms in 3 beads.
but in dist.xv file,there ware two peaks,in other words,i had two angle that have most distribution.
which angle should i use?
Last edit: 10 years 7 months ago by msaeedi.
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- Clement
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10 years 7 months ago #1867
by Clement
Replied by Clement on topic angle parameter in cg topology
There's no right answer to that; it depends the values your angle takes. Are the distributions equivalent (equal in height) for both peaks? Is the total distribution symmetric, i.e. with main peaks at +/-90° for instance? Are you sure to have a sufficiently converged AA simulation to define your distribution/angles?
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- msaeedi
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10 years 7 months ago #1881
by msaeedi
Replied by msaeedi on topic angle parameter in cg topology
Hi, Thanks for your response.
I did a 100ns AA simulation and the angle distribution was symmetric and one peak was higher than another. I think, I must choose the higher peak and put it in topology file and suggest k angle and k improper dihedral and after that do a cg simulation.
i have a question about improving parameters. Is it correct to do cg simulation without using Reverse transformation tool? Is it correct to do em(steep),nvt,npt,md cg simulation and then compare bonded parameters with AA simulation?
I did a 100ns AA simulation and the angle distribution was symmetric and one peak was higher than another. I think, I must choose the higher peak and put it in topology file and suggest k angle and k improper dihedral and after that do a cg simulation.
i have a question about improving parameters. Is it correct to do cg simulation without using Reverse transformation tool? Is it correct to do em(steep),nvt,npt,md cg simulation and then compare bonded parameters with AA simulation?
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- djurre
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10 years 7 months ago #1888
by djurre
Replied by djurre on topic angle parameter in cg topology
Yes, that is the right thing to do: the reverse transformation you run only once (to get a CG trajectory from you AA, as a reference) and after that you do the CG simulations without the Ref-Trans tool. The order of the simulations you mention is also correct, although for most CG simulations NVT relaxation doesn't add to much, imho.
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- msaeedi
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10 years 7 months ago #1889
by msaeedi
Replied by msaeedi on topic angle parameter in cg topology
Thanks for your response.
I have a question about changing angle parameter.
I prepared a cg topology and did a cg simulation. Angle parameter changed very much. For example, I choose 110 degree for one angle and k angle= 35 KJ/mol and after cg simulation it changed to 35 degree.
How should I change angle parameter to reach to corresponding AA simulation?
Should I change k angle or angle to reach to corresponding AA simulation?
I have a question about changing angle parameter.
I prepared a cg topology and did a cg simulation. Angle parameter changed very much. For example, I choose 110 degree for one angle and k angle= 35 KJ/mol and after cg simulation it changed to 35 degree.
How should I change angle parameter to reach to corresponding AA simulation?
Should I change k angle or angle to reach to corresponding AA simulation?
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