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Regarding the last MARTINI parameters for DOPC
- Stéfane
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8 years 5 months ago - 8 years 5 months ago #5186
by Stéfane
Regarding the last MARTINI parameters for DOPC was created by Stéfane
Dear all,
I am confused with the updated DOPC Martini parameters available here : md.chem.rug.nl/index.php/force-field-par...ml?dir=PC&lipid=DOPC since it is stated that the DOPC is a di-C16:1-C18:1 PC instead of a di-C18:1 PC. By checking the corresponding itp file "martini_v2.0_DOPC_02.itp" I have found that the molecule is represented with only 12 beads in contrast to the older one (martini_v2.0_lipids.itp that have 14 beads). The position of the double bonds is also different in the two parameters
;@RESNTEST DOP==DOPC if: atoms[0]==NC3
DOPC 1
1 Q0 1 DOPC NC3 1 1.0
2 Qa 1 DOPC PO4 2 -1.0
3 Na 1 DOPC GL1 3 0
4 Na 1 DOPC GL2 4 0
5 C1 1 DOPC C1A 5 0
6 C3 1 DOPC D2A 6 0
7 C1 1 DOPC C3A 7 0
8 C1 1 DOPC C4A 8 0
9 C1 1 DOPC C1B 9 0
10 C3 1 DOPC D2B 10 0
11 C1 1 DOPC C3B 11 0
12 C1 1 DOPC C4B 12 0
in martini_v2.0_lipids.itp
;;;;;; COMMON PCs: DPPC, DHPC, DLPC (DMPC), DSPC, POPC, DOPC, DAPC, DUPC
DOPC
1 Q0 1 DOPC NC3 1 1.0
2 Qa 1 DOPC PO4 2 -1.0
3 Na 1 DOPC GL1 3 0
4 Na 1 DOPC GL2 4 0
5 C1 1 DOPC C1A 5 0
6 C1 1 DOPC C2A 6 0
7 C3 1 DOPC D3A 7 0
8 C1 1 DOPC C4A 8 0
9 C1 1 DOPC C5A 9 0
10 C1 1 DOPC C1B 10 0
11 C1 1 DOPC C2B 11 0
12 C3 1 DOPC D3B 12 0
13 C1 1 DOPC C4B 13 0
14 C1 1 DOPC C5B 14 0
Moreover by reading the insane.py file I have found that DOPC is modeled with only 12 beads
"DOPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B D2B C3B C4B - - "),
Since I used the older DOPC parameters with 14 beads in my simulations (as for instance in a recent paper (10.1039/c5sm01350j), I am afraid that my simulations are not correct. Could you explain to me these differences.
Thanks
Stéfane
I am confused with the updated DOPC Martini parameters available here : md.chem.rug.nl/index.php/force-field-par...ml?dir=PC&lipid=DOPC since it is stated that the DOPC is a di-C16:1-C18:1 PC instead of a di-C18:1 PC. By checking the corresponding itp file "martini_v2.0_DOPC_02.itp" I have found that the molecule is represented with only 12 beads in contrast to the older one (martini_v2.0_lipids.itp that have 14 beads). The position of the double bonds is also different in the two parameters
;@RESNTEST DOP==DOPC if: atoms[0]==NC3
DOPC 1
1 Q0 1 DOPC NC3 1 1.0
2 Qa 1 DOPC PO4 2 -1.0
3 Na 1 DOPC GL1 3 0
4 Na 1 DOPC GL2 4 0
5 C1 1 DOPC C1A 5 0
6 C3 1 DOPC D2A 6 0
7 C1 1 DOPC C3A 7 0
8 C1 1 DOPC C4A 8 0
9 C1 1 DOPC C1B 9 0
10 C3 1 DOPC D2B 10 0
11 C1 1 DOPC C3B 11 0
12 C1 1 DOPC C4B 12 0
in martini_v2.0_lipids.itp
;;;;;; COMMON PCs: DPPC, DHPC, DLPC (DMPC), DSPC, POPC, DOPC, DAPC, DUPC
DOPC
1 Q0 1 DOPC NC3 1 1.0
2 Qa 1 DOPC PO4 2 -1.0
3 Na 1 DOPC GL1 3 0
4 Na 1 DOPC GL2 4 0
5 C1 1 DOPC C1A 5 0
6 C1 1 DOPC C2A 6 0
7 C3 1 DOPC D3A 7 0
8 C1 1 DOPC C4A 8 0
9 C1 1 DOPC C5A 9 0
10 C1 1 DOPC C1B 10 0
11 C1 1 DOPC C2B 11 0
12 C3 1 DOPC D3B 12 0
13 C1 1 DOPC C4B 13 0
14 C1 1 DOPC C5B 14 0
Moreover by reading the insane.py file I have found that DOPC is modeled with only 12 beads
"DOPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B D2B C3B C4B - - "),
Since I used the older DOPC parameters with 14 beads in my simulations (as for instance in a recent paper (10.1039/c5sm01350j), I am afraid that my simulations are not correct. Could you explain to me these differences.
Thanks
Stéfane
Last edit: 8 years 5 months ago by Stéfane.
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- helgi
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8 years 5 months ago #5189
by helgi
Replied by helgi on topic Regarding the last MARTINI parameters for DOPC
Hello, hello,
This is indeed confusing. The old DOPC has x14 beads (x5 beads per tail) but the new DOPC has x4 beads per tail (x12 beads total). Neither one is wrong; the new one is a little bit more correct. Due to the coarse mapping of Martini and building block strategy lipid tail will always jump in size by 4C tail atoms per x1 CG bead and DOPC (C18 tail) fall in the middle (x5 tail beads are to many, x4 are to few). If you are starting a new project I would use the new DOPC (x12 beads total) but if you are continuing a project or comparing to old date be consistent (e.g. continue using the old DOPC). Apart from thickens there are some more subtle differences e.g. new DOPC phase separation should be slightly more realistic.
The old DOPC is also in insane.py but instead of using –l DOPC you have to use –l DOPC.o
Hope this clears this up,
Cheers,
- Helgi
This is indeed confusing. The old DOPC has x14 beads (x5 beads per tail) but the new DOPC has x4 beads per tail (x12 beads total). Neither one is wrong; the new one is a little bit more correct. Due to the coarse mapping of Martini and building block strategy lipid tail will always jump in size by 4C tail atoms per x1 CG bead and DOPC (C18 tail) fall in the middle (x5 tail beads are to many, x4 are to few). If you are starting a new project I would use the new DOPC (x12 beads total) but if you are continuing a project or comparing to old date be consistent (e.g. continue using the old DOPC). Apart from thickens there are some more subtle differences e.g. new DOPC phase separation should be slightly more realistic.
The old DOPC is also in insane.py but instead of using –l DOPC you have to use –l DOPC.o
Hope this clears this up,
Cheers,
- Helgi
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- Stéfane
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8 years 5 months ago #5190
by Stéfane
Replied by Stéfane on topic Regarding the last MARTINI parameters for DOPC
OK thanks Helgi, for the clarification.
Stefane
Stefane
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