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Picking Angle in Martini
- mohammadsb
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8 years 6 months ago #5177
by mohammadsb
Picking Angle in Martini was created by mohammadsb
Hi,
Is anybody knows how we pick angles in Martini forcefield? I am trying to implement Martini forcefield in my MC code.
I noticed some of angle parameters have not been defined in Martini forcefield and coupling 1-3 interaction with angle energy would not give me correct distribution compare to MD code.
For example in picking angle for C1-C1-C1, MD(NAMD) code shows highest probability of picking 150 degree and my code shows 180. Here is My BONDED and NONBONDED parameters in Charmm format and my calculation for angle and 1-3 nonbonded energy.
I would appreciate if someone could help me.
BONDS
C1 C1 1.4937859 4.8 ! Dry Martini
ANGLES
C1 C1 C1 4.18260038 180 cos ! Dry Martini
NONBONDED
C1 C1 -1.075525812 5.2755716 ! Dry Martin II
at theta = 150, angle energy is 37.7 K, 1-3 nonbonded energy is -32.22 K => sum = 5.48
at theta = 180, angle energy is 0.0 K, 1-3 nonbonded energy is -14.3 K => sum = -14.3
So, it is more favorable to pick 180 instead of 150.
Is anybody knows how we pick angles in Martini forcefield? I am trying to implement Martini forcefield in my MC code.
I noticed some of angle parameters have not been defined in Martini forcefield and coupling 1-3 interaction with angle energy would not give me correct distribution compare to MD code.
For example in picking angle for C1-C1-C1, MD(NAMD) code shows highest probability of picking 150 degree and my code shows 180. Here is My BONDED and NONBONDED parameters in Charmm format and my calculation for angle and 1-3 nonbonded energy.
I would appreciate if someone could help me.
BONDS
C1 C1 1.4937859 4.8 ! Dry Martini
ANGLES
C1 C1 C1 4.18260038 180 cos ! Dry Martini
NONBONDED
C1 C1 -1.075525812 5.2755716 ! Dry Martin II
at theta = 150, angle energy is 37.7 K, 1-3 nonbonded energy is -32.22 K => sum = 5.48
at theta = 180, angle energy is 0.0 K, 1-3 nonbonded energy is -14.3 K => sum = -14.3
So, it is more favorable to pick 180 instead of 150.
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- siewert
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8 years 5 months ago #5238
by siewert
Replied by siewert on topic Picking Angle in Martini
Hi,
it is not clear what you mean - which system are you simulating here?
And what do you mean by 'picking'?
In Martini all angles are usually defined
Please clarify ...
Siewert-Jan
it is not clear what you mean - which system are you simulating here?
And what do you mean by 'picking'?
In Martini all angles are usually defined
Please clarify ...
Siewert-Jan
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