- Posts: 40
Benzene, density and surface tension.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2317
by panzu
Benzene, density and surface tension. was created by panzu
Hello all users,
I am traying to reproduce the next experiment.
A simulation of a system containing
400 CG water molecules and 400 benzene molecules, at a temperature
T=293 K and pressure P=1 bar. Starting from randomly
mixed conditions, the oily and aqueous phases rapidly demix
into two slabs similar to the geometry.
(I am following the same steps as in "The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations". Phys. Chem. B 2007,111,7812-7824
Section 3.3Extension to Ringlike Compounds. 3.3.1. Cyclohexane
and Benzene.)
I take the followings force fields:
martini_v2.0.itp
martini_v2.0_solvents.itp
I use a time step dt= 0.030 ps
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = BENZ W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.5 1.5
ref_t = 293 293
Pcoupl = berendsen
Pcoupltype = isotropic ;semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0 ;3.0
compressibility = 1.0e-5 ;1.0
ref_p = 1.0 ;1.0
However I can not obtain the same density as in the paper (0.72g/cm³), instead I get 1.2g/cm³. Neither I get the proper surface tension (Water-Benzene) according to experimental results (38 mN/m), instead I get 80 mN/m.
So if somebody could help my with this problem it would be appreciated!
I am traying to reproduce the next experiment.
A simulation of a system containing
400 CG water molecules and 400 benzene molecules, at a temperature
T=293 K and pressure P=1 bar. Starting from randomly
mixed conditions, the oily and aqueous phases rapidly demix
into two slabs similar to the geometry.
(I am following the same steps as in "The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations". Phys. Chem. B 2007,111,7812-7824
Section 3.3Extension to Ringlike Compounds. 3.3.1. Cyclohexane
and Benzene.)
I take the followings force fields:
martini_v2.0.itp
martini_v2.0_solvents.itp
I use a time step dt= 0.030 ps
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = BENZ W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.5 1.5
ref_t = 293 293
Pcoupl = berendsen
Pcoupltype = isotropic ;semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0 ;3.0
compressibility = 1.0e-5 ;1.0
ref_p = 1.0 ;1.0
However I can not obtain the same density as in the paper (0.72g/cm³), instead I get 1.2g/cm³. Neither I get the proper surface tension (Water-Benzene) according to experimental results (38 mN/m), instead I get 80 mN/m.
So if somebody could help my with this problem it would be appreciated!
Please Log in or Create an account to join the conversation.
- nanogod
-
- Offline
- Senior Boarder
Less
More
10 years 6 months ago #2318
by nanogod
Replied by nanogod on topic Benzene, density and surface tension.
I am no sure, but try adding water with -vdwd 0.21. This will set the radius of the pseudo-atom for the water molecule to 0.21 nm instead of gromacs defaults.
Kind regards
Nanogod
Kind regards
Nanogod
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
10 years 6 months ago #2319
by djurre
Replied by djurre on topic Benzene, density and surface tension.
Many things might be going wrong here, but most likely: As is stated in the martini_v2.0_solvents.itp, we changed the beadtype of Benzene. From SC4 to SC5. Could that explain the difference?
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2321
by panzu
Replied by panzu on topic Benzene, density and surface tension.
Well, I had had into acount the change from SC4 to SC5 in martini_v2.0_solvents.itp
Please Log in or Create an account to join the conversation.
- siewert
-
- Offline
- Admin
Less
More
- Posts: 61
10 years 6 months ago #2367
by siewert
Replied by siewert on topic Benzene, density and surface tension.
First, you should use semi-isotropic pressure coupling in this system, fixing the lateral directions (setting compressibility to 0.0) and coupling the perpendicular direction (assuming it is the z-direction) to 1 bar. Then you should get the correct surface tension from the pressure differences between the lateral and perpendicular directions.
Second, for a correct density, make sure you use realistic masses in the simlation, or scale with the real masses afterwards. Remember Martini uses default masses for the particles.
Good luck!
Second, for a correct density, make sure you use realistic masses in the simlation, or scale with the real masses afterwards. Remember Martini uses default masses for the particles.
Good luck!
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2369
by panzu
Replied by panzu on topic Benzene, density and surface tension.
So, Benzene , which is mostly 3 beads in triangle, has a mass of 45 uma per bead, then, should I change the value of the mass of a bead by a real value according to the bead?
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
10 years 6 months ago #2370
by jaakko
Replied by jaakko on topic Benzene, density and surface tension.
You can either change the masses of the beads to be molecular mass of benzene divided by three or scale the density you get afterwards by the ratio of real molecular mass divided by 3*45 amu.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2475
by panzu
Replied by panzu on topic Benzene, density and surface tension.
Everything is all right now.
Thank you!!
Thank you!!
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2537
by panzu
Replied by panzu on topic Benzene, density and surface tension.
About the calculation of surface tension, something might be going wrong:
Firstly I had simulated a system of Benzene and Water with a comperssibility of 3.0e-4 bar-1 (as Martini suggests)
md.chem.rug.nl/cgmartini/index.php/force...ers/input-parameters
The simulation box was streched in z direction and got shorter in X-Y direction such as the simulation even crashed due to the short length of X-Y direcction. I repeated the simulation, I took a larger sistem (3456 Benzenes and 7606 Waters and 844 anti-frozen Water,lx=ly=5.95 and lz=49.6, 2 water slab of 15 nm,1 Benzene slab of 16 nm) also I did another simulation with comperssibility of 3.0e-4 but again I had the same problem.
Next I performed another simulation, I fixed the comperssibility at X/Y direcction equal to 0 as you adviced me. The problem was solved, the length at X-Y direction was conserverd but the barostat did not yield a correct pressure:
Statistics over 4125501 steps [ 0.0000 through 123765.0000 ps ], 4 data sets
All statistics are over 412551 points
Energy Average Err.Est. RMSD Tot-Drift
Pressure -5.95364 0.085 30.6296 0.0410342 (bar)
Pres-XX -9.39876 0.17 40.0578 0.0983339 (bar)
Pres-YY -9.4879 0.098 40.1115 0.0243231 (bar)
Pres-ZZ 1.02573 0.00031 41.5075 0.000445658 (bar)
Here are the parameters I asked for:
; RUN CONTROL PARAMETERS =
integrator = md
tinit = 0
dt = 0.030
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = V-rescale
; Groups to couple separately =
tc-grps = BENZ W WF
; Time constant (ps) and reference temperature (K) =
tau_t = 0.5 0.5 0.5
ref_t = 300 300 300
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 5.0 5.0
compressibility = 0 3e-4
ref_p = 1.0 1.0
Does anybody know why this happen?
thanks for your kind help in advance
Firstly I had simulated a system of Benzene and Water with a comperssibility of 3.0e-4 bar-1 (as Martini suggests)
md.chem.rug.nl/cgmartini/index.php/force...ers/input-parameters
The simulation box was streched in z direction and got shorter in X-Y direction such as the simulation even crashed due to the short length of X-Y direcction. I repeated the simulation, I took a larger sistem (3456 Benzenes and 7606 Waters and 844 anti-frozen Water,lx=ly=5.95 and lz=49.6, 2 water slab of 15 nm,1 Benzene slab of 16 nm) also I did another simulation with comperssibility of 3.0e-4 but again I had the same problem.
Next I performed another simulation, I fixed the comperssibility at X/Y direcction equal to 0 as you adviced me. The problem was solved, the length at X-Y direction was conserverd but the barostat did not yield a correct pressure:
Statistics over 4125501 steps [ 0.0000 through 123765.0000 ps ], 4 data sets
All statistics are over 412551 points
Energy Average Err.Est. RMSD Tot-Drift
Pressure -5.95364 0.085 30.6296 0.0410342 (bar)
Pres-XX -9.39876 0.17 40.0578 0.0983339 (bar)
Pres-YY -9.4879 0.098 40.1115 0.0243231 (bar)
Pres-ZZ 1.02573 0.00031 41.5075 0.000445658 (bar)
Here are the parameters I asked for:
; RUN CONTROL PARAMETERS =
integrator = md
tinit = 0
dt = 0.030
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = V-rescale
; Groups to couple separately =
tc-grps = BENZ W WF
; Time constant (ps) and reference temperature (K) =
tau_t = 0.5 0.5 0.5
ref_t = 300 300 300
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 5.0 5.0
compressibility = 0 3e-4
ref_p = 1.0 1.0
Does anybody know why this happen?
thanks for your kind help in advance
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 6 months ago #2539
by xavier
Replied by xavier on topic Benzene, density and surface tension.
Your system is 15(water)+16(benzene)=31 nm on the z direction but lz=49.6 nm ... did you let the system equilibrate before measuring the pressure?
panzu wrote: About the calculation of surface tension, something might be going wrong:
Firstly I had simulated a system of Benzene and Water with a comperssibility of 3.0e-4 bar-1 (as Martini suggests)
md.chem.rug.nl/cgmartini/index.php/force...ers/input-parameters
The simulation box was streched in z direction and got shorter in X-Y direction such as the simulation even crashed due to the short length of X-Y direcction. I repeated the simulation, I took a larger sistem (3456 Benzenes and 7606 Waters and 844 anti-frozen Water,lx=ly=5.95 and lz=49.6, 2 water slab of 15 nm,1 Benzene slab of 16 nm) also I did another simulation with comperssibility of 3.0e-4 but again I had the same problem.
Next I performed another simulation, I fixed the comperssibility at X/Y direcction equal to 0 as you adviced me. The problem was solved, the length at X-Y direction was conserverd but the barostat did not yield a correct pressure:
Statistics over 4125501 steps [ 0.0000 through 123765.0000 ps ], 4 data sets
All statistics are over 412551 points
Energy Average Err.Est. RMSD Tot-Drift
Pressure -5.95364 0.085 30.6296 0.0410342 (bar)
Pres-XX -9.39876 0.17 40.0578 0.0983339 (bar)
Pres-YY -9.4879 0.098 40.1115 0.0243231 (bar)
Pres-ZZ 1.02573 0.00031 41.5075 0.000445658 (bar)
Here are the parameters I asked for:
; RUN CONTROL PARAMETERS =
integrator = md
tinit = 0
dt = 0.030
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = V-rescale
; Groups to couple separately =
tc-grps = BENZ W WF
; Time constant (ps) and reference temperature (K) =
tau_t = 0.5 0.5 0.5
ref_t = 300 300 300
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 5.0 5.0
compressibility = 0 3e-4
ref_p = 1.0 1.0
Does anybody know why this happen?
thanks for your kind help in advance
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2540
by panzu
Replied by panzu on topic Benzene, density and surface tension.
I have a slab of Water(≈15 nm) then a slab of Benzene(≈16nm) and another slab of Water(≈15 nm). Yes, I did equilibrate the system before.
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 6 months ago #2541
by xavier
Replied by xavier on topic Benzene, density and surface tension.
Ok so you've got 15+16+15=46 nm.
The pressure you report is indeed off! Did you remove the "equilibration" phase before calculation? Did you try to see weather the pressure was stable at that value or the magnitude you measure is simply due to fluctuations? In other words: Could you detail the manner you determine the pressure.
The pressure you report is indeed off! Did you remove the "equilibration" phase before calculation? Did you try to see weather the pressure was stable at that value or the magnitude you measure is simply due to fluctuations? In other words: Could you detail the manner you determine the pressure.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2542
by panzu
Replied by panzu on topic Benzene, density and surface tension.
well, I did a NVT calibration of the system, next I did a NPT calibration and last I started measuring the pressure.
The pressure is stable at that point, I can not see why.
The pressure is stable at that point, I can not see why.
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 6 months ago #2543
by xavier
Replied by xavier on topic Benzene, density and surface tension.
My question is now more on how you determined the pressure you reported. How long is the period used for the average? Is it evolving over that period?
Is it starting with the right values at the end of the NPD run and then deviating?
I am asking because an non-equilibrated pressure in the x,y plane might be difficult to relax with a zero compressibility.
Is it starting with the right values at the end of the NPD run and then deviating?
I am asking because an non-equilibrated pressure in the x,y plane might be difficult to relax with a zero compressibility.
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2545
by panzu
Replied by panzu on topic Benzene, density and surface tension.
I got a period of a point per each 100 step of MD for the use of the averages.
You are right, as I start from a non-equilibrated pressure in the x,y plane and I fix zero compressibility at X-Y plane, the system can not relax properly.
So the point is, How can I relax the X-Y plane? As I said before, when I use a semi-isotropic barostat with a compressibility of 3.0e-4 at X-Y plane, the simulation box is streched in z direction and X-Y plane gets shorter up to the crashing of the simulation.
So what can I do in order to relax the x-Y plane? Should I use a isotropic barostat then?
You are right, as I start from a non-equilibrated pressure in the x,y plane and I fix zero compressibility at X-Y plane, the system can not relax properly.
So the point is, How can I relax the X-Y plane? As I said before, when I use a semi-isotropic barostat with a compressibility of 3.0e-4 at X-Y plane, the simulation box is streched in z direction and X-Y plane gets shorter up to the crashing of the simulation.
So what can I do in order to relax the x-Y plane? Should I use a isotropic barostat then?
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 6 months ago #2546
by xavier
Replied by xavier on topic Benzene, density and surface tension.
Here is my interpretation of what you observe:
In an homogeneous system the z direction should compensate for the lake of compressibility on the x/y directions. You could try with a water box to check. However you have an interface water/benzene with a surface tension. The system will try to reduce the size of this interface to its minimum. It is probably why you observe a shrinkage of the x/y dimension.
I guess that if you have reached an equilibrated x/y and z pressure you should be able to extract the surface tension :))
In an homogeneous system the z direction should compensate for the lake of compressibility on the x/y directions. You could try with a water box to check. However you have an interface water/benzene with a surface tension. The system will try to reduce the size of this interface to its minimum. It is probably why you observe a shrinkage of the x/y dimension.
I guess that if you have reached an equilibrated x/y and z pressure you should be able to extract the surface tension :))
panzu wrote: I got a period of a point per each 100 step of MD for the use of the averages.
You are right, as I start from a non-equilibrated pressure in the x,y plane and I fix zero compressibility at X-Y plane, the system can not relax properly.
So the point is, How can I relax the X-Y plane? As I said before, when I use a semi-isotropic barostat with a compressibility of 3.0e-4 at X-Y plane, the simulation box is streched in z direction and X-Y plane gets shorter up to the crashing of the simulation.
So what can I do in order to relax the x-Y plane? Should I use a isotropic barostat then?
Please Log in or Create an account to join the conversation.
- panzu
-
Topic Author
- Visitor
10 years 6 months ago #2547
by panzu
Replied by panzu on topic Benzene, density and surface tension.
That makes sense.
So,should I equilibrate Water and Benzen slab apart and then put them together?
So,should I equilibrate Water and Benzen slab apart and then put them together?
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 6 months ago #2553
by xavier
Replied by xavier on topic Benzene, density and surface tension.
Does it make sense?
You do not need to equilibrate them separately because they will equilibrate together anyway and the disparity between the expected value and the observed values are the result of surface tension ...
You do not need to equilibrate them separately because they will equilibrate together anyway and the disparity between the expected value and the observed values are the result of surface tension ...
panzu wrote: That makes sense.
So,should I equilibrate Water and Benzen slab apart and then put them together?
Please Log in or Create an account to join the conversation.
Time to create page: 0.122 seconds