- Posts: 8
density of oleyl laurate
- meganS
-
Topic Author
- Offline
- Fresh Boarder
Less
More
9 years 8 months ago #4033
by meganS
density of oleyl laurate was created by meganS
Dear all,
i have one question here, what should i do if the coarse-grained structure which i produced did not show similar density with the experimental one?
the experimental density is 0.865 but i get 0.748.
this is how i calculate it -> density that i get from g_energy (1076.81) was divided by (72 amu * no. of atom; in my case 9). the value obtained then multiplied by olayl laurate molecular weight..
i have one question here, what should i do if the coarse-grained structure which i produced did not show similar density with the experimental one?
the experimental density is 0.865 but i get 0.748.
this is how i calculate it -> density that i get from g_energy (1076.81) was divided by (72 amu * no. of atom; in my case 9). the value obtained then multiplied by olayl laurate molecular weight..
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
9 years 8 months ago #4039
by xavier
Replied by xavier on topic density of oleyl laurate
The difference is 0.865-0.748=0.117 so about 14% off. This is not great but still.
What about you change the typography of your molecule?
What about the different mdp options you have? All good?
What about you change the typography of your molecule?
What about the different mdp options you have? All good?
meganS wrote: Dear all,
i have one question here, what should i do if the coarse-grained structure which i produced did not show similar density with the experimental one?
the experimental density is 0.865 but i get 0.748.
this is how i calculate it -> density that i get from g_energy (1076.81) was divided by (72 amu * no. of atom; in my case 9). the value obtained then multiplied by olayl laurate molecular weight..
Please Log in or Create an account to join the conversation.
- meganS
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
9 years 8 months ago #4041
by meganS
Replied by meganS on topic density of oleyl laurate
Hi Xavier, thanks alot for your prompt reply.
the mdp file that i used was from this website. the mdp file for GROMACS 4.0..
i am so sorry,i am not so clear about the typography, what should i change actually?
the mdp file that i used was from this website. the mdp file for GROMACS 4.0..
i am so sorry,i am not so clear about the typography, what should i change actually?
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
9 years 8 months ago #4042
by xavier
Replied by xavier on topic density of oleyl laurate
The typography is the bead type assigned to the particle constituting your molecule. The strength of the self-self interaction will affect the density. Thus by tuning the typography of the molecule you can affect the density of the system. Note that this should also be in balance with interactions with other particle types: other solvents are generally used to tune this based on solvation free energies and differences between solvents.
Check one of the papers/review on Martini to have a better idea.
Check one of the papers/review on Martini to have a better idea.
meganS wrote: Hi Xavier, thanks alot for your prompt reply.
the mdp file that i used was from this website. the mdp file for GROMACS 4.0..
i am so sorry,i am not so clear about the typography, what should i change actually?
Please Log in or Create an account to join the conversation.
- meganS
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
9 years 8 months ago #4043
by meganS
Replied by meganS on topic density of oleyl laurate
Hi, noted that. i'll check the papers. Thank you so much.
Please Log in or Create an account to join the conversation.
- mnmelo
-
- Offline
- Admin
Less
More
- Posts: 89
9 years 8 months ago #4044
by mnmelo
Replied by mnmelo on topic density of oleyl laurate
Hi,
A couple of mapping suggestions more particular to your case:
As you know, the typical Martini mapping is roughly 4-to-1. At 32 heavy atoms you should be aiming for 8 Martini beads. 9 is probably too much, and that is probably why you're getting too low a density.
That said, when dealing with alkanes you'll probably want to keep to the standard topology as much as possible (bead type C1 for saturated beads, 0.47nm bond length, 1250kJ/mol force constant, etc. -- check the available topologies for inspiration). This will ensure the greatest transferability of properties when interacting with the rest of the Martini world.
For your particular case I suggest the following:
- One Na bead for the esther link (comprising the esther carbon, the two oxygens, and one carbon on the oleyl side). This is the mapping used for phospholipid esther bonds.
- Three C1 beads for the remaining 11 carbons of the laurate chain.
- Four beads for the remaining 17 oleyl carbons. I'd assign the unsaturated bead as the second from the esther, and either a C3 or a C4 type. The rest should be C1.
You should be able to find out the rest of the bonded parameters you need from the alkane and phospholipid topologies. Be sure to apply a 120 degrees angle potential over the cis double bond -- check the DOPC topology for the parameters; in that case 5 beads are used for the oleyl chain but we're recently moving towards only 4.
You'll notice that for phospholipids there's no angle potential over esther links; you might find that one is required to reproduce atomistic distributions, and I'd love to hear from you on this respect.
Finally, you might then hit the granularity of alkane mapping when using Martini: chains of 10, 11, 12, 13 or 14 carbons may all be represented by three beads. Of course all these different alkanes will have different properties but they will all be the same in Martini. With the mapping as I suggested I think this will have a minor effect.
Do give feedback,
Manel
A couple of mapping suggestions more particular to your case:
As you know, the typical Martini mapping is roughly 4-to-1. At 32 heavy atoms you should be aiming for 8 Martini beads. 9 is probably too much, and that is probably why you're getting too low a density.
That said, when dealing with alkanes you'll probably want to keep to the standard topology as much as possible (bead type C1 for saturated beads, 0.47nm bond length, 1250kJ/mol force constant, etc. -- check the available topologies for inspiration). This will ensure the greatest transferability of properties when interacting with the rest of the Martini world.
For your particular case I suggest the following:
- One Na bead for the esther link (comprising the esther carbon, the two oxygens, and one carbon on the oleyl side). This is the mapping used for phospholipid esther bonds.
- Three C1 beads for the remaining 11 carbons of the laurate chain.
- Four beads for the remaining 17 oleyl carbons. I'd assign the unsaturated bead as the second from the esther, and either a C3 or a C4 type. The rest should be C1.
You should be able to find out the rest of the bonded parameters you need from the alkane and phospholipid topologies. Be sure to apply a 120 degrees angle potential over the cis double bond -- check the DOPC topology for the parameters; in that case 5 beads are used for the oleyl chain but we're recently moving towards only 4.
You'll notice that for phospholipids there's no angle potential over esther links; you might find that one is required to reproduce atomistic distributions, and I'd love to hear from you on this respect.
Finally, you might then hit the granularity of alkane mapping when using Martini: chains of 10, 11, 12, 13 or 14 carbons may all be represented by three beads. Of course all these different alkanes will have different properties but they will all be the same in Martini. With the mapping as I suggested I think this will have a minor effect.
Do give feedback,
Manel
Please Log in or Create an account to join the conversation.
- meganS
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
9 years 7 months ago #4056
by meganS
Replied by meganS on topic density of oleyl laurate
Hi mnmelo,
Thanks alot for your reply. i am working on it, surely, i will give the feedback once i am done.
Thanks alot for your reply. i am working on it, surely, i will give the feedback once i am done.
Please Log in or Create an account to join the conversation.
Time to create page: 0.090 seconds