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- A small doubt regarding actual bead mass and default considered bead mass
A small doubt regarding actual bead mass and default considered bead mass
- sdutta
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1 year 6 days ago #9608
by sdutta
A small doubt regarding actual bead mass and default considered bead mass was created by sdutta
Hello, I am a beginner with Martini simulation. I have one very general question regarding parameterize of a small molecule .
When we are considering the beads, default mass of R, S and T beads are considered. For example T beads are considered with mass 36 amu. In principle though it is written that mass of the beads are sum of mass of constituent atoms, but I didn't find at any example of
github.com/ricalessandri/Martini3-small-molecules where proper bead mass are used. In this way I am trying to simulate liquid benzene with three T beads having mass 36 amu, but I am ending up at wrong density which is almost 0.722 times scaled with respect to actual density.
Please help me out to figure it out this issue.
When we are considering the beads, default mass of R, S and T beads are considered. For example T beads are considered with mass 36 amu. In principle though it is written that mass of the beads are sum of mass of constituent atoms, but I didn't find at any example of
github.com/ricalessandri/Martini3-small-molecules where proper bead mass are used. In this way I am trying to simulate liquid benzene with three T beads having mass 36 amu, but I am ending up at wrong density which is almost 0.722 times scaled with respect to actual density.
Please help me out to figure it out this issue.
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- vainikka
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1 year 6 days ago #9609
by vainikka
Replied by vainikka on topic A small doubt regarding actual bead mass and default considered bead mass
Hi.
For density, you'll have to assign the beads correct masses. You can just add the mass for each bead in the .itp, so that instead of having:
1 TC5 1 BENZ R1 1 0
etc.
you'd have:
1 TC5 1 BENZ R1 1 0 26
etc.
which would roughly correspond to the sum of the masses of the constituent atoms.
For density, you'll have to assign the beads correct masses. You can just add the mass for each bead in the .itp, so that instead of having:
1 TC5 1 BENZ R1 1 0
etc.
you'd have:
1 TC5 1 BENZ R1 1 0 26
etc.
which would roughly correspond to the sum of the masses of the constituent atoms.
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- sdutta
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11 months 3 weeks ago #9619
by sdutta
Replied by sdutta on topic A small doubt regarding actual bead mass and default considered bead mass
Hi Vainikka,
Thank you so much for your reply. I am getting a strange result for simulating liquid benzene, if I use constraints in between the assigned beads, I am getting density that is pretty close to the experimental one.
But I wanted to cross check the result with bonds, I am using hermonic bonds in between the beads with the force constant around 200000 kj/mol/nm^2 and the timestep is 1 fs. Ideally it should work if I compare with my AA simulations.
But I am finally getting the average density of liquid benzene around 276 kg/m^3. This is very surprising to me. I am using the bead mass 26 amu as well.
Please let me know if something is inconsistent.
Thank you so much for your reply. I am getting a strange result for simulating liquid benzene, if I use constraints in between the assigned beads, I am getting density that is pretty close to the experimental one.
But I wanted to cross check the result with bonds, I am using hermonic bonds in between the beads with the force constant around 200000 kj/mol/nm^2 and the timestep is 1 fs. Ideally it should work if I compare with my AA simulations.
But I am finally getting the average density of liquid benzene around 276 kg/m^3. This is very surprising to me. I am using the bead mass 26 amu as well.
Please let me know if something is inconsistent.
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