- Posts: 70
Further information in: The MARTINI Force Field
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2870
by panzu
Further information in: The MARTINI Force Field was created by panzu
Hello all users,
I am wondering if you could clarify me the next question:
The TABLE 4 of the paper, The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations,reports results about the Surface Tension of the water/vapor, dodecane/vapor and the Interfacial Tension between dodecane/water.
There is data about the system such as: Small system (400 CG beads per solvent phase) and large system (1600 CG beads), but in fact, it is not as important the number of CG beads of the system as the size of the system.
Therefore, I would like to get further information, in particulary, I would like to know how large the simulation box is for the dodecane/water interface.
Thanks in advance!
I am wondering if you could clarify me the next question:
The TABLE 4 of the paper, The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations,reports results about the Surface Tension of the water/vapor, dodecane/vapor and the Interfacial Tension between dodecane/water.
There is data about the system such as: Small system (400 CG beads per solvent phase) and large system (1600 CG beads), but in fact, it is not as important the number of CG beads of the system as the size of the system.
Therefore, I would like to get further information, in particulary, I would like to know how large the simulation box is for the dodecane/water interface.
Thanks in advance!
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
10 years 5 months ago #2872
by jaakko
Replied by jaakko on topic Further information in: The MARTINI Force Field
Hi panzu,
I don't really understand your question. The number of beads of solvent directly correlates with the volume of the system in constant pressure. A few tens of ns of equilibration of a solvent box with 400/1600 beads should give you your answer. Just build the system and try, you'll have your answer after a coffee break.
Just to give you an idea of the length scale, the equilibrated box of 400 CG waters in this website is a cube with each side about 3.6 nm.
I don't really understand your question. The number of beads of solvent directly correlates with the volume of the system in constant pressure. A few tens of ns of equilibration of a solvent box with 400/1600 beads should give you your answer. Just build the system and try, you'll have your answer after a coffee break.
Just to give you an idea of the length scale, the equilibrated box of 400 CG waters in this website is a cube with each side about 3.6 nm.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2873
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
My point is, you have to make sure that each side in your simulation box have a length of at least 10*sigma or 15*sigma in order to obtain a good characterization of the interface, otherwise you would get correlation via pressure ... given you a bad interface measurment.
Neither I think you would get bulk property with such as small size...
Neither I think you would get bulk property with such as small size...
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
10 years 5 months ago #2874
by jaakko
Replied by jaakko on topic Further information in: The MARTINI Force Field
You're right, you have to account for that. Using a different sized boxes to calculate the same property is a useful tool to evaluate this. The paper does discuss this:
Hope this helped with your question.
Emphasis mine, quote from the 2007 Martini paper.In order to study size effects, both a small system (400 CG beads per solvent phase) and a large system (1600 beads) were simulated. Simulations of 1 μs proved long enough to accurately calculate the interfacial tension. The results are summarized in Table 4. Finite size effects are actually important when calculating the interfacial tension. The tension is systematically smaller for the larger system size. We attribute this to the development of capillary waves which are supressed in the small system. Additional simulations for even larger systems show no further decrease of the measured tension.
Hope this helped with your question.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2876
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
If you Increased the size in all directions, yes, I agree. That is what I wanted to know.
Thanks a lot.
Thanks a lot.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2891
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
Well, May I ask another question about this?
The paper says that the working temperature is 293 K. So I believe you used antifreezen water in the water slab in order to avoid the solid state, right?
The paper says that the working temperature is 293 K. So I believe you used antifreezen water in the water slab in order to avoid the solid state, right?
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2893
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
In fact I do not understand why your water is freezen between 280 K and 300 K. If you plot the L-J diagram for water with epsilon=5.0 kJ/mol and sigma=0.47 nm and truncate it at 2.5*sigma you find the solid state at 1 bar from 330 K to backward
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 5 months ago #2895
by xavier
Replied by xavier on topic Further information in: The MARTINI Force Field
The use of antifreeze particles is indeed recommended at low temperature. It should be mentioned in the paper ... not sure which section you are looking at.
You have to be careful on the definition of sigma=0.47 nm. It is the minimum of the potential and not the crossing with the Epot=0.
The us of a shift function of the LJ potential also modifies the potential. That might need to be taken into account also. You can try to print the actual potential within GMX.
You have to be careful on the definition of sigma=0.47 nm. It is the minimum of the potential and not the crossing with the Epot=0.
The us of a shift function of the LJ potential also modifies the potential. That might need to be taken into account also. You can try to print the actual potential within GMX.
panzu wrote: In fact I do not understand why your water is freezen between 280 K and 300 K. If you plot the L-J diagram for water with epsilon=5.0 kJ/mol and sigma=0.47 nm and truncate it at 2.5*sigma you find the solid state at 1 bar from 330 K to backward
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2934
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
Yes, I meant with sigma as the minimum of the potential.
What I had ploted was the phase diagrams of the shifted and truncated LJ at 1.175 nm epsilon=5.0 kJ/mol (of water) Maybe that is why I got a larger freezen point.
What I had ploted was the phase diagrams of the shifted and truncated LJ at 1.175 nm epsilon=5.0 kJ/mol (of water) Maybe that is why I got a larger freezen point.
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 5 months ago #2937
by xavier
Not sure what you mean here ...
Replied by xavier on topic Further information in: The MARTINI Force Field
panzu wrote: What I had ploted was the phase diagrams of the shifted and truncated LJ at 1.175 nm epsilon=5.0 kJ/mol (of water) Maybe that is why I got a larger freezen point.
Not sure what you mean here ...
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2944
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
well, I mean how the phase diagram for water in your model looks like.
I plotted the phase diagriam (melting line or freezing line in a P-T plot) and using a shifted LJ at 1.175 nm and epsilon=5.0 kJ/mol I get that the water is frozen at 330K while in your model the water freezes between 280K - 300K.
Am I missing something?
I plotted the phase diagriam (melting line or freezing line in a P-T plot) and using a shifted LJ at 1.175 nm and epsilon=5.0 kJ/mol I get that the water is frozen at 330K while in your model the water freezes between 280K - 300K.
Am I missing something?
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
10 years 5 months ago #2947
by jaakko
Hi panzu,
it's hard to say what's the difference since I don't know how exactly you calculate the phase diagram. Obvious differences are that you say you shift at 1.175 nm (2.5 sigma). I don't know why you do this but assume it has something to do with your calculation. So there's clearly differences between how the shiften LJ in Martini (as implemented in GROMACS) looks like and what you calculate. Also note that the shift in GROMACS isn't just a shift of the potential. Another thing that I think I mentioned already earlier is the artificial ordering due to periodic effects. I have no tangible to show what the effect of that on freezing point is but I'd hazard a guess you'll see a significant difference in the freezing temperatures if you compare very small boxes of water to large ones.
Replied by jaakko on topic Further information in: The MARTINI Force Field
panzu wrote: well, I mean how the phase diagram for water in your model looks like.
I plotted the phase diagriam (melting line or freezing line in a P-T plot) and using a shifted LJ at 1.175 nm and epsilon=5.0 kJ/mol I get that the water is frozen at 330K while in your model the water freezes between 280K - 300K.
Am I missing something?
Hi panzu,
it's hard to say what's the difference since I don't know how exactly you calculate the phase diagram. Obvious differences are that you say you shift at 1.175 nm (2.5 sigma). I don't know why you do this but assume it has something to do with your calculation. So there's clearly differences between how the shiften LJ in Martini (as implemented in GROMACS) looks like and what you calculate. Also note that the shift in GROMACS isn't just a shift of the potential. Another thing that I think I mentioned already earlier is the artificial ordering due to periodic effects. I have no tangible to show what the effect of that on freezing point is but I'd hazard a guess you'll see a significant difference in the freezing temperatures if you compare very small boxes of water to large ones.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 5 months ago #2948
by panzu
Replied by panzu on topic Further information in: The MARTINI Force Field
Ok, I see that the difference does not only come from where I shift the LJ as I suspect.
Thanks!!
Thanks!!
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 4 months ago #2953
by xavier
Replied by xavier on topic Further information in: The MARTINI Force Field
The shift of LJ potential starts at 0.9 nm. It is also called switch function in other "software". Check the manual for the exact formula.
panzu wrote: Ok, I see that the difference does not only come from where I shift the LJ as I suspect.
Thanks!!
Please Log in or Create an account to join the conversation.
- Pim
-
- Offline
- Expert Boarder
Less
More
- Posts: 105
5 years 5 months ago #7851
by Pim
Replied by Pim on topic Further information in: The MARTINI Force Field
I'm not sure why you are posting here... Clearly we are talking about the martini force field. I don't know the Trappe ff and whether it's implemented in grimace you'd have to ask the gromacs mailing list. I've never heard about it.
Please Log in or Create an account to join the conversation.
Time to create page: 0.112 seconds