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lipids
- c.poojari
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12 years 8 months ago #757
by c.poojari
lipids was created by c.poojari
Hello,
I have just switched from atomistic simulations to coarse grained simulations.
I want to set up a mixed bilayer system. In the martini_v2.0_lipids.itp file which i downloaded from the martini tutorial page, i didnt find POPS and Phosphatidylinositol lipids. Please can i know if these lipids are available to download ????
Also please can I know if the .itp files available on the tutorial page the latest ones or are they any new .itp files updated with more lipids and modified paramters.
Kind regards,
chetan
I have just switched from atomistic simulations to coarse grained simulations.
I want to set up a mixed bilayer system. In the martini_v2.0_lipids.itp file which i downloaded from the martini tutorial page, i didnt find POPS and Phosphatidylinositol lipids. Please can i know if these lipids are available to download ????
Also please can I know if the .itp files available on the tutorial page the latest ones or are they any new .itp files updated with more lipids and modified paramters.
Kind regards,
chetan
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- siewert
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12 years 8 months ago #758
by siewert
Replied by siewert on topic lipids
POPS is there (at the end of the martini_v2.0_lipids.itp file), download it from the Download section and you will have the latest version.
PIs are currently being parameterized. If you want a trial topology, send an email to:
Cesar Lopez <This email address is being protected from spambots. You need JavaScript enabled to view it.>.
In general the itp files on the web contain the latest parameters, but the files in the Tutorial section might be older versions.
Thanks for pointing this out!
PIs are currently being parameterized. If you want a trial topology, send an email to:
Cesar Lopez <This email address is being protected from spambots. You need JavaScript enabled to view it.>.
In general the itp files on the web contain the latest parameters, but the files in the Tutorial section might be older versions.
Thanks for pointing this out!
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- c.poojari
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12 years 8 months ago #759
by c.poojari
Replied by c.poojari on topic lipids
Dear Marrink,
I have downloaded the latest version of lipid itp files. Also contacted Cesar Lopez for Phosphatidylinositol lipids.
I want to setup a mixed bilayer simulation with 1500 lipids (3 different lipids, cholesterol and sphingolpids). Based on area per lipid, for 1500 lipids i got box dimensions of 32.5 X 32.5 X 8 nm. As i was going through one of your papers on "Simulation of Domain Formation in DLPCâDSPC Mixed Bilayers" you had used 2048 lipids with box dimension of 22 X 23 X 8 nm.
Please can I know how do i calculate proper box dimension for lipids ???
While generating desired number of lipids starting from a single lipid as mentioned in the tutorial, should i have same box size for all the lipids, cholesterol and sphingolipids as i want to cat them later so that i have one large box containing all the lipids and then do minimization.
or is there any other way where i can add all the different number of lipids and simulate them for self assembly.
Kind Regards,
chetan.
I have downloaded the latest version of lipid itp files. Also contacted Cesar Lopez for Phosphatidylinositol lipids.
I want to setup a mixed bilayer simulation with 1500 lipids (3 different lipids, cholesterol and sphingolpids). Based on area per lipid, for 1500 lipids i got box dimensions of 32.5 X 32.5 X 8 nm. As i was going through one of your papers on "Simulation of Domain Formation in DLPCâDSPC Mixed Bilayers" you had used 2048 lipids with box dimension of 22 X 23 X 8 nm.
Please can I know how do i calculate proper box dimension for lipids ???
While generating desired number of lipids starting from a single lipid as mentioned in the tutorial, should i have same box size for all the lipids, cholesterol and sphingolipids as i want to cat them later so that i have one large box containing all the lipids and then do minimization.
or is there any other way where i can add all the different number of lipids and simulate them for self assembly.
Kind Regards,
chetan.
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