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benzene density
- minsari
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10 years 6 months ago #2597
by minsari
benzene density was created by minsari
Dear all users,
I am a beginner for GROMACS as well as MARTINI forcefield, but this website is a great help to understand and try some CGMD simulation. (Many thanks.)
I have a question about the density of MARTINI CGMD.
When I attempted to execute a example application for "polystyrene in bezene" in this website, I realized that the density of whole system was quite high.
So, I set up a simulation box with 5000 molecules of benzene to confirm the density of benzene. I got an average density, 1227.97 kg/m^3 for CG benzene. It is quite different from experimental density as well as Marrink's results (JPCB 2007, 111, 7812).
The procedures are as follows.
1. genbox ( 5000 molecules of BENZ )
2. EM
3. NVT - short
4. NPT ( t-coupl: v-rescale 300 K, P-coupl: prarrinello-rahman 1 bar, 5 ns )
5. g_energy -> average density calculation
Is there any missing part when I simulate or calculate the density?
Best regards,
minsari
I am a beginner for GROMACS as well as MARTINI forcefield, but this website is a great help to understand and try some CGMD simulation. (Many thanks.)
I have a question about the density of MARTINI CGMD.
When I attempted to execute a example application for "polystyrene in bezene" in this website, I realized that the density of whole system was quite high.
So, I set up a simulation box with 5000 molecules of benzene to confirm the density of benzene. I got an average density, 1227.97 kg/m^3 for CG benzene. It is quite different from experimental density as well as Marrink's results (JPCB 2007, 111, 7812).
The procedures are as follows.
1. genbox ( 5000 molecules of BENZ )
2. EM
3. NVT - short
4. NPT ( t-coupl: v-rescale 300 K, P-coupl: prarrinello-rahman 1 bar, 5 ns )
5. g_energy -> average density calculation
Is there any missing part when I simulate or calculate the density?
Best regards,
minsari
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- panzu
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10 years 5 months ago #2869
by panzu
Replied by panzu on topic benzene density
Hello ,
Sorry for the late replay...
I exactly got the same when I first simulated benzene.
Martini use a default molecular masses in the martini*.itp(you can check it, they are 72 for the other molecules and 45 for ring configuration) so you just scale the masses and get the density that is said in the paper.
So, you divide this density by 45 time the number of atom that benzene has (3 atomos) and multiply for the real molecular mass of the benzene,78.11. At the end you will get 710 kg/m³ more or less like the paper says.
Sorry for the late replay...
I exactly got the same when I first simulated benzene.
Martini use a default molecular masses in the martini*.itp(you can check it, they are 72 for the other molecules and 45 for ring configuration) so you just scale the masses and get the density that is said in the paper.
So, you divide this density by 45 time the number of atom that benzene has (3 atomos) and multiply for the real molecular mass of the benzene,78.11. At the end you will get 710 kg/m³ more or less like the paper says.
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- xavier
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10 years 5 months ago #2898
by xavier
Replied by xavier on topic benzene density
Indeed the correction of the masses of the beads should fix the problem.
Thanks Panzu for your answer.
Thanks Panzu for your answer.
panzu wrote: Hello ,
Sorry for the late replay...
I exactly got the same when I first simulated benzene.
Martini use a default molecular masses in the martini*.itp(you can check it, they are 72 for the other molecules and 45 for ring configuration) so you just scale the masses and get the density that is said in the paper.
So, you divide this density by 45 time the number of atom that benzene has (3 atomos) and multiply for the real molecular mass of the benzene,78.11. At the end you will get 710 kg/m³ more or less like the paper says.
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- panzu
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10 years 5 months ago #2933
by panzu
Replied by panzu on topic benzene density
It costs nothing. :)
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