Trappe Cyclohexane
- MonteCarlo83
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7 years 9 months ago #211
by MonteCarlo83
Dear Cassandra-Developers and users,
I started to simulate Cyclohexane in the GEMC ensemble (your example) and in the NpT-Ensemble (1 bar and 298.15 K).
When I visualize the ensembles, I get very flat benzene-like molecules, which is kind of strange to me. Does not the Trappe force field give the right structure for cyclohexane or did I have make any mistakes.
For the NpT-ensemble I took your mcf-file and psb-file for creating a fragment library and for the GEMC ensemble I just used your example.
Best regards,
Mark
I started to simulate Cyclohexane in the GEMC ensemble (your example) and in the NpT-Ensemble (1 bar and 298.15 K).
When I visualize the ensembles, I get very flat benzene-like molecules, which is kind of strange to me. Does not the Trappe force field give the right structure for cyclohexane or did I have make any mistakes.
For the NpT-ensemble I took your mcf-file and psb-file for creating a fragment library and for the GEMC ensemble I just used your example.
Best regards,
Mark
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- emarin
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7 years 9 months ago #214
by emarin
Hi Mark!
There is an error in the input MCF dihedral parameters. Cassandra by default uses an OPLS functional form of the type
c0+c1[1+cos(ϕ)]+c2[1−cos(2ϕ)]+c3[1+cos(3ϕ)]
while the TraPPE cyclohexane dihedral functional form is
c0+c1cos(ϕ)+c2cos(2ϕ)+c3cos(3ϕ)
I did a quick conversion between the functional forms and I got the following parameters
Cyclohexane [K] OPLS[K] OPLS[KJ/mol]
c0 5073 1736 14.43
c1 6840 6840 56.87
c2 3509 -3509 -29.17
c3 63 63 0.5239
Can you confirm this numbers and see if you get right conformations?
Thanks!
There is an error in the input MCF dihedral parameters. Cassandra by default uses an OPLS functional form of the type
c0+c1[1+cos(ϕ)]+c2[1−cos(2ϕ)]+c3[1+cos(3ϕ)]
while the TraPPE cyclohexane dihedral functional form is
c0+c1cos(ϕ)+c2cos(2ϕ)+c3cos(3ϕ)
I did a quick conversion between the functional forms and I got the following parameters
Cyclohexane [K] OPLS[K] OPLS[KJ/mol]
c0 5073 1736 14.43
c1 6840 6840 56.87
c2 3509 -3509 -29.17
c3 63 63 0.5239
Can you confirm this numbers and see if you get right conformations?
Thanks!
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- MonteCarlo83
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7 years 9 months ago #217
by MonteCarlo83
Hi,
I just calculated the parameters again. For c0 I get 13.959 kJ/mol.
I have the same values for the c1,c2 and c3.
I just started a new NpT with the new calculated parameters and after a quick check
the simulations started from the expected chair-like conformations (in contrast to the simulations with the wrong parameters).
Thanks a lot!
Best regards,
Mark
I just calculated the parameters again. For c0 I get 13.959 kJ/mol.
I have the same values for the c1,c2 and c3.
I just started a new NpT with the new calculated parameters and after a quick check
the simulations started from the expected chair-like conformations (in contrast to the simulations with the wrong parameters).
Thanks a lot!
Best regards,
Mark
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- emarin
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