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water beads W crystallize on a graphene plane
- exianshine
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11 years 3 months ago #1321
by exianshine
water beads W crystallize on a graphene plane was created by exianshine
I am simulating a system combined of a graphene plane and waters on the surface of it.
PBC is used. and NPzAT ensemble is used.
however after 1microsecond, the water crystalized in the system and there is a big hole in the icy water, does anyone know this strange things?
thanks!
PBC is used. and NPzAT ensemble is used.
however after 1microsecond, the water crystalized in the system and there is a big hole in the icy water, does anyone know this strange things?
thanks!
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- djurre
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11 years 3 months ago #1322
by djurre
Replied by djurre on topic water beads W crystallize on a graphene plane
Martini water has a slightly too high freezing point. Especially when large surfaces are present in the system it might freeze at/around room temperature. You can solve this by using "anti-freeze particles". Replace 10% of your water (W) by the antifreeze particles (WF). Due their slightly larger radius the packing is disturbed and the freezing temperature becomes higher.
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- siewert
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11 years 3 months ago #1323
by siewert
Replied by siewert on topic water beads W crystallize on a graphene plane
Another option is to use the polarizable water model, which has a lower melting point.
See: S.O. Yesylevskyy, L.V. Schäfer, D. Sengupta, S.J. Marrink. Polarizable water model for the coarse-grained Martini force field. PLoS Comp. Biol, 6:e1000810, 2010.
See: S.O. Yesylevskyy, L.V. Schäfer, D. Sengupta, S.J. Marrink. Polarizable water model for the coarse-grained Martini force field. PLoS Comp. Biol, 6:e1000810, 2010.
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- exianshine
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11 years 3 months ago #1324
by exianshine
Replied by exianshine on topic water beads W crystallize on a graphene plane
Thanks for your replies. I tried another way to solve this problem.
I reduced the interaction strength of the P4-P4 type beads to 76% of original. which is suggest by
Fluid Phase Equilib. 2007 December 1; 261(1-2): 18–25.
It works fine now. thanks!
I reduced the interaction strength of the P4-P4 type beads to 76% of original. which is suggest by
Fluid Phase Equilib. 2007 December 1; 261(1-2): 18–25.
It works fine now. thanks!
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- siewert
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11 years 3 months ago #1326
by siewert
Replied by siewert on topic water beads W crystallize on a graphene plane
That is a bad solution, and is not recommended by us!
If you reduce the P4-P4 interaction, you should realize that you do no longer simulate water, but a less polar fluid like propanol or something instead ....
If you reduce the P4-P4 interaction, you should realize that you do no longer simulate water, but a less polar fluid like propanol or something instead ....
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- exianshine
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11 years 3 months ago #1327
by exianshine
Replied by exianshine on topic water beads W crystallize on a graphene plane
Thanks for your reply.
I think maybe in my situation this is possible, the reason for this point is below.
I just changed the P4-P4 interaction. I did not change the interaction strength with other beads type (for example the beads of the plane, which has no P4 type beads).
What I care is not the behavior of water, but the behavior of the solutes in the water. the interaction of the water with the solutes is not changed.
Do you think it is proper to use this?
I think maybe in my situation this is possible, the reason for this point is below.
I just changed the P4-P4 interaction. I did not change the interaction strength with other beads type (for example the beads of the plane, which has no P4 type beads).
What I care is not the behavior of water, but the behavior of the solutes in the water. the interaction of the water with the solutes is not changed.
Do you think it is proper to use this?
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11 years 3 months ago #1329
by siewert
Replied by siewert on topic water beads W crystallize on a graphene plane
If you change the water-water interaction, it will also change the hydration free energy of other solutes and hence their partitioning behavior - you will bias the propensity of your solutes to self-assemble, or to bind to the surface ...
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11 years 3 months ago #1332
by exianshine
Replied by exianshine on topic water beads W crystallize on a graphene plane
Thanks for your reply.
In this way, maybe I should consider the model of water.
I have tried the anti-freeze water beads, how ever, the crystall of water still exist.
Maybe I should try the polar model of water? In that way the computation duty is so large.
That a big problem, I think
In this way, maybe I should consider the model of water.
I have tried the anti-freeze water beads, how ever, the crystall of water still exist.
Maybe I should try the polar model of water? In that way the computation duty is so large.
That a big problem, I think
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