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Change DSPC to POPC lipid
- thu nguyen
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11 years 2 months ago - 11 years 2 months ago #1396
by thu nguyen
Change DSPC to POPC lipid was created by thu nguyen
Dear all,
I want to change my DSPC bilayer to POPC bilayer. I saw the guiding for changing DSPC to DOPC in tutorial. But DSPC and DOPC have the same number of atom. While POPC has one atom less than DSPC. What should i do in this case ?
Thankful for any advice !
Regards,
KT
I want to change my DSPC bilayer to POPC bilayer. I saw the guiding for changing DSPC to DOPC in tutorial. But DSPC and DOPC have the same number of atom. While POPC has one atom less than DSPC. What should i do in this case ?
Thankful for any advice !
Regards,
KT
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- djurre
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11 years 2 months ago #1397
by djurre
Replied by djurre on topic Change DSPC to POPC lipid
Remove the surplus beads from you gro file. Either by hand or using a smart grep command.
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- sudel
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11 years 1 month ago #1422
by sudel
Replied by sudel on topic Change DSPC to POPC lipid
Hi All,
How to do reverse i,e POPC to DSPC? In my case, I want to convert DPPC to DOPC. These two lipids are differed by two beads. However, DPPC has 2 bead smaller than DOPC. Moreover, I wish to convert a .gro file of DPPC to .gro file of DOPC where the number of water and ions will remain same for these two systems.
sudel
How to do reverse i,e POPC to DSPC? In my case, I want to convert DPPC to DOPC. These two lipids are differed by two beads. However, DPPC has 2 bead smaller than DOPC. Moreover, I wish to convert a .gro file of DPPC to .gro file of DOPC where the number of water and ions will remain same for these two systems.
sudel
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- djurre
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11 years 1 month ago #1423
by djurre
Replied by djurre on topic Change DSPC to POPC lipid
I can't think of a fast and easy way to do this. I would probably write a script that moves all the lipids in one monolayer up/down in order to create a gap and than add the extra beads at geometric positions in between. The water can be added back afterwards, making sure the number of waters is the same with genbox.
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- sudel
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11 years 1 month ago #1425
by sudel
Replied by sudel on topic Change DSPC to POPC lipid
How to add the water molecules exactly by genbox. Can you please specify it.
Another thing, I have prepared a big box by replicating a small box in x and y direction using genconf. However, it does not arrange the lipids and water molecule. Is there any gromacs tool that does it very easily?
How do I add ions in that system by using gromacs tool?
Another thing, I have prepared a big box by replicating a small box in x and y direction using genconf. However, it does not arrange the lipids and water molecule. Is there any gromacs tool that does it very easily?
How do I add ions in that system by using gromacs tool?
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11 years 1 month ago #1426
by djurre
Tutorial 1A. Do set the new box size (-box) in order to get a proper new box size.
You can use g_select/make_ndx + trjconv, but it is probably faster to use grep:
and then adopt your top file accordingly.
Try:
Replied by djurre on topic Change DSPC to POPC lipid
sudel wrote: How to add the water molecules exactly by genbox. Can you please specify it.
Tutorial 1A. Do set the new box size (-box) in order to get a proper new box size.
sudel wrote: Another thing, I have prepared a big box by replicating a small box in x and y direction using genconf. However, it does not arrange the lipids and water molecule. Is there any gromacs tool that does it very easily?
You can use g_select/make_ndx + trjconv, but it is probably faster to use grep:
head -2 OLD.gro > new.gro
grep DOPC OLD.gro >> new.gro
grep W OLD.gro >> new.gro
tail -1 OLD.gro > new.groand then adopt your top file accordingly.
sudel wrote: How do I add ions in that system by using gromacs tool?
Try:
genion -hPlease Log in or Create an account to join the conversation.
- sudel
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11 years 1 month ago #1428
by sudel
Replied by sudel on topic Change DSPC to POPC lipid
Somehow, I have managed a system that contain 1024 DOPC lipid, water and 0.15 (M) NaCl. I was getting the area per lipid for this system at around 70.0. However, the experimental value is 72.4. Can anyone provide a reference that contain this information for MARTINI DOPC lipid.
Sudel
Sudel
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- xavier
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11 years 1 month ago #1430
by xavier
Replied by xavier on topic Change DSPC to POPC lipid
Not sure what is the exact area per lipid for DOPC in MARTINI but 70.0 for a value of 72.4 is a rather good match.
Note that the [NaCl] will have an effect on the area/lipid.
Note that the [NaCl] will have an effect on the area/lipid.
sudel wrote: Somehow, I have managed a system that contain 1024 DOPC lipid, water and 0.15 (M) NaCl. I was getting the area per lipid for this system at around 70.0. However, the experimental value is 72.4. Can anyone provide a reference that contain this information for MARTINI DOPC lipid.
Sudel
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