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coarse graining dichlorobenzene
- meganS
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10 years 3 months ago #3410
by meganS
coarse graining dichlorobenzene was created by meganS
Hi. Firstly, i'd like to say thank you to the team for providing this page. It is truly help me to get to know MARTINI force field,
Currently, i want to coarse grain dichlorobenzene structure, however in MARTINI paper (2007) there is no x-c=c group, as it only has x-c-c.
can i just use x-c-c to map the structure?
Currently, i want to coarse grain dichlorobenzene structure, however in MARTINI paper (2007) there is no x-c=c group, as it only has x-c-c.
can i just use x-c-c to map the structure?
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10 years 3 months ago #3420
by siewert
Replied by siewert on topic coarse graining dichlorobenzene
Looking at experimental solubility data, dichlorobenzene is less soluble in water than benzene (about 100 mg/L versus 1.8 g/L). Therefore I would model 1,2-dichlorobenzene with two SC4 particle types (representative of the x-c-c group) and one SC5 particle (note: standard benzene is modeled with three SC5 particles in Martini 2.2). In case of 1,4-dichlorobenzene I would keep the symmetry and convert all particles to SC4 type.
Given the bulkiness of the chloro substituent, one could change the SC4 beads to normal C4 beads to improve the density of the bulk liquid. Note that this would also affect the solubility. A simulation of the bulk liquid in equilibrium with bulk water, or a more fancy free energy perturbation method, should show you whether this is required or not.
Given the bulkiness of the chloro substituent, one could change the SC4 beads to normal C4 beads to improve the density of the bulk liquid. Note that this would also affect the solubility. A simulation of the bulk liquid in equilibrium with bulk water, or a more fancy free energy perturbation method, should show you whether this is required or not.
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10 years 3 months ago #3425
by meganS
Replied by meganS on topic coarse graining dichlorobenzene
Thank you so much, siewert.
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10 years 2 months ago #3509
by meganS
Replied by meganS on topic coarse graining dichlorobenzene
Hi,
i have another question here, i am a little bit unsure of this thing:
i tried to coarse grained a molecule which has an ionic part : RCOO- , O- will have nonbonded interaction with Na+,
is Na (C-0-C=O)
group is applicable to this case?
Thank you,
MS
i have another question here, i am a little bit unsure of this thing:
i tried to coarse grained a molecule which has an ionic part : RCOO- , O- will have nonbonded interaction with Na+,
is Na (C-0-C=O)
group is applicable to this case?
Thank you,
MS
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10 years 2 months ago #3522
by meganS
Replied by meganS on topic coarse graining dichlorobenzene
Hi,Thank you so much, siewert.
i have another question here, i am a little bit unsure of this thing:
i tried to coarse grained a molecule which has an ionic part : RCOO- , O- will have nonbonded interaction with Na+,
is Na (C-0-C=O)
group is applicable to this case?
Thank you,
MS
i have another question here, i am a little bit unsure of this thing:
i tried to coarse grained a molecule which has an ionic part : RCOO- , O- will have nonbonded interaction with Na+,
is Na (C-0-C=O)
group is applicable to this case?
Thank you,
MS
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10 years 2 months ago #3524
by siewert
Replied by siewert on topic coarse graining dichlorobenzene
I am not sure what you mean. The R-C-O-O- group should be modeled as a Qa particle,
and a sodium ion as Qd.
Or do you imply that a strong salt-bridge is formed an you would like to model the R-C-O-O--Na+ as a single bead? In that case you should try to embed charged particles as we did in case of polar side cahins in Martini 2.2. Alternatively, you could simply add a (short) bond between the Qa and Qd particle to enforce the salt bridge.
and a sodium ion as Qd.
Or do you imply that a strong salt-bridge is formed an you would like to model the R-C-O-O--Na+ as a single bead? In that case you should try to embed charged particles as we did in case of polar side cahins in Martini 2.2. Alternatively, you could simply add a (short) bond between the Qa and Qd particle to enforce the salt bridge.
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