- Posts: 19
questions about the MFFA boundary condition
- richor
-
Topic Author
- Offline
- Fresh Boarder
Less
More
10 years 11 months ago #1574
by richor
questions about the MFFA boundary condition was created by richor
Hi,Martini users:
Is there anyone who has used the MFFA boundary condition to simulate a vesicle?
I'm just come across it and have some confusions.
I have read the paper introducing it --Risselada et al. (2008) Application of mean field boundary potentials in simulations of lipid vesicles. J Phys Chem B 112:7438-7447
Then I download the necessary files from md.chem.rug.nl/~mara/mffa.html#howto .
In the example provided,a dopc vesicle was presented.I ran it successfully.
To run it, the water.sdb and lipid.sdb must be provided.
Following that,I want to simulate some other lipid moleculars, but I'm not sure the lipid.sdb still work.
If it doesn't work any more,how can I generate it for other lipid molecular?
Any suggestion will be greatly appreciated!
--Richor
Is there anyone who has used the MFFA boundary condition to simulate a vesicle?
I'm just come across it and have some confusions.
I have read the paper introducing it --Risselada et al. (2008) Application of mean field boundary potentials in simulations of lipid vesicles. J Phys Chem B 112:7438-7447
Then I download the necessary files from md.chem.rug.nl/~mara/mffa.html#howto .
In the example provided,a dopc vesicle was presented.I ran it successfully.
To run it, the water.sdb and lipid.sdb must be provided.
Following that,I want to simulate some other lipid moleculars, but I'm not sure the lipid.sdb still work.
If it doesn't work any more,how can I generate it for other lipid molecular?
Any suggestion will be greatly appreciated!
--Richor
Please Log in or Create an account to join the conversation.
- xavier
-
- Offline
- Admin
Less
More
- Posts: 416
10 years 11 months ago #1580
by xavier
Replied by xavier on topic questions about the MFFA boundary condition
unfortunately the people working on this have left the lab ... please give detail on your progress that we can all learn from you :))
What is the content of lipid.sdb
What is the content of lipid.sdb
richor wrote: Hi,Martini users:
Is there anyone who has used the MFFA boundary condition to simulate a vesicle?
I'm just come across it and have some confusions.
I have read the paper introducing it --Risselada et al. (2008) Application of mean field boundary potentials in simulations of lipid vesicles. J Phys Chem B 112:7438-7447
Then I download the necessary files from md.chem.rug.nl/~mara/mffa.html#howto .
In the example provided,a dopc vesicle was presented.I ran it successfully.
To run it, the water.sdb and lipid.sdb must be provided.
Following that,I want to simulate some other lipid moleculars, but I'm not sure the lipid.sdb still work.
If it doesn't work any more,how can I generate it for other lipid molecular?
Any suggestion will be greatly appreciated!
--Richor
Please Log in or Create an account to join the conversation.
- siewert
-
- Offline
- Admin
Less
More
- Posts: 61
10 years 11 months ago #1587
by siewert
Replied by siewert on topic questions about the MFFA boundary condition
In the "sdb" files, the actual MFFA potential is given. For lipids, only a purely repulsive potential is used to avoid them sticking to the MFFA boundary.
This potential can be used for any type of lipid, so no need to modify "lipid.sdb".
This potential can be used for any type of lipid, so no need to modify "lipid.sdb".
Please Log in or Create an account to join the conversation.
Time to create page: 0.101 seconds