- Posts: 10
Something about bilayer spontaneous-assembly
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
11 years 11 months ago #937
by Ray
Something about bilayer spontaneous-assembly was created by Ray
I am currently trying to selfassemble a 512 lipid bilayer consisting of DPPC lipids.I tried different ways include spontaneous-assembly from single dppc,enlarge bilayer from 128 DPPC to 512 DPPC and using packmol tools. However, there still exists a problem that water are probably in one side and some lipids run out of the bilayer.
My problem is same to the previous topic "512 DPPG bilayer", but i didn't use the polarized water.
I‘m looking forward very much to your kind reply.
Best regards.
My problem is same to the previous topic "512 DPPG bilayer", but i didn't use the polarized water.
I‘m looking forward very much to your kind reply.
Best regards.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 11 months ago #938
by djurre
Replied by djurre on topic Something about bilayer spontaneous-assembly
The easiest way to get a 512 DPPC lipid bilayer would be to start from the existing 128 lipid bilayer you can download from the website (Downloads >> Example applications) and use the Gromacs tool 'genconf' to multiply it 4 times. Does that work?
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 11 months ago #948
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Thank you very much for your reply!
Yes,I have tried that way.I made the 512 lipid bilayer by expanding a 128 bilayer in the x and y direction using "genconf".The problem is the bilayer is not a symmetrical system after 40ns equilibrium in which water is probably in one side and some lipids run out of the bilayer.What's the problem?
Yes,I have tried that way.I made the 512 lipid bilayer by expanding a 128 bilayer in the x and y direction using "genconf".The problem is the bilayer is not a symmetrical system after 40ns equilibrium in which water is probably in one side and some lipids run out of the bilayer.What's the problem?
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 11 months ago #951
by djurre
Replied by djurre on topic Something about bilayer spontaneous-assembly
That is very strange, this bilayer has been used for this many times. You mention there is water in one side of the bilayer. I would expect it to be expelled quickly, but maybe if it is a lot it could disturb the bilayer a lot?
In the original 128 DPPC bilayer there was no water in the bilayer. Are you solvating the bilayer after you have multiplied it? Because you shouldn't: the system already contains water.
In the original 128 DPPC bilayer there was no water in the bilayer. Are you solvating the bilayer after you have multiplied it? Because you shouldn't: the system already contains water.
Please Log in or Create an account to join the conversation.
- siewert
-
- Offline
- Admin
Less
More
- Posts: 61
11 years 11 months ago #952
by siewert
Replied by siewert on topic Something about bilayer spontaneous-assembly
I think you are fooled by the periodic boundary conditions - if you shift the bilayer in the box (or use VMD to visualize the system with periodic images) you will see that the bilayer is perfectly allright!
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 11 months ago #955
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear djurre：
Firstly I will still show my deep gratitude for your concern to my problem.
I'm afraid I have not made myself clear. Can you see the figure attach to the email ? I mean the lipid bilayer is probably OK in my system except some lipids run out of the bilayer. The main question is the water. Water is not on either hand of bilayer . They are almost on one hand of the bilayer! There is no water in the bilayer.
Firstly I will still show my deep gratitude for your concern to my problem.
I'm afraid I have not made myself clear. Can you see the figure attach to the email ? I mean the lipid bilayer is probably OK in my system except some lipids run out of the bilayer. The main question is the water. Water is not on either hand of bilayer . They are almost on one hand of the bilayer! There is no water in the bilayer.
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 11 months ago #956
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear siewert：
Thank you very much！
I also suspect the periodic boundary conditions in the beginning. The periodic images is not good enough because there are some lipids out of bilayer. What do you mean by "shift the bilayer in the box"?
Thank you very much！
I also suspect the periodic boundary conditions in the beginning. The periodic images is not good enough because there are some lipids out of bilayer. What do you mean by "shift the bilayer in the box"?
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 11 months ago #957
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
I did it！Thank you so much for your suggestion.
Please Log in or Create an account to join the conversation.
- richor
-
- Offline
- Fresh Boarder
Less
More
- Posts: 19
11 years 7 months ago #1108
by richor
Replied by richor on topic Something about bilayer spontaneous-assembly
Dear djurre:
I have a question here.
Would there be a artificial periodic if we multiply the 128 system to 512?
For larger systems like 6000,will the effect be smaller?
Appreciate for your reply!
I have a question here.
Would there be a artificial periodic if we multiply the 128 system to 512?
For larger systems like 6000,will the effect be smaller?
Appreciate for your reply!
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 7 months ago #1111
by djurre
Replied by djurre on topic Something about bilayer spontaneous-assembly
There will be some periodic effect due to the repeated patterns. However these repeated patterns will soon been lost (of some tens of nanoseconds I would say). If the effect is more or less in a bigger system I don't know.
Please Log in or Create an account to join the conversation.
- richor
-
- Offline
- Fresh Boarder
Less
More
- Posts: 19
11 years 7 months ago #1112
by richor
Replied by richor on topic Something about bilayer spontaneous-assembly
Thank you so much.
As we are using the Periodic Boundary Conditions,I cannot figure out why the patterns will be
lost.I have looked through the Gromacs tutorial,no clue was found.
Can you help me?
Best regards!
As we are using the Periodic Boundary Conditions,I cannot figure out why the patterns will be
lost.I have looked through the Gromacs tutorial,no clue was found.
Can you help me?
Best regards!
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 7 months ago #1113
by djurre
Replied by djurre on topic Something about bilayer spontaneous-assembly
Maybe I misunderstood. You are copying the system in the XY-plane (for example with genconf)? The periodicity that you see in the generated starting structure will disappear quickly when you once you start simulating, because the lipids in the system all move differently.
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 5 months ago #1254
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear Djurre：
I have recently got some problems when I tried to establish a relative large lipid bilayer system. So could I ask you a favor?
I wanted to build the system including 1152 lipid molecules. But I failed to get a plane lipid bilayer. In the first case, there are 1152lipids and 20000 water,the bilayer is not a single plane,it is just like a irregular lipid system mixed up with two bilayers. I then added more water molecules to 60000. I surprised to get a cylindric bilayer. It so confused me. Could you please help me check this question whether there are some details I have not noticed.
I'm looking forward very much to your kind reply.
Best regards.
Sincerely yours,
Ray
I have recently got some problems when I tried to establish a relative large lipid bilayer system. So could I ask you a favor?
I wanted to build the system including 1152 lipid molecules. But I failed to get a plane lipid bilayer. In the first case, there are 1152lipids and 20000 water,the bilayer is not a single plane,it is just like a irregular lipid system mixed up with two bilayers. I then added more water molecules to 60000. I surprised to get a cylindric bilayer. It so confused me. Could you please help me check this question whether there are some details I have not noticed.
I'm looking forward very much to your kind reply.
Best regards.
Sincerely yours,
Ray
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 4 months ago #1291
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear Djurre：
I'm sorry to reply later. You still remember my "cool" lipid bilayer? I have done that by enlarging the system "128 lipids" with "genconf" to "1152 lipids" system as the method you mentioned. However, I still can't obtain a plain bilayer. I think the problem exisited after energy minimization. After energy minimization, the lipid molecules moved to the surface of the box, which might lead to a cylindric bilayer. What's your opinion?
I'm sorry to reply later. You still remember my "cool" lipid bilayer? I have done that by enlarging the system "128 lipids" with "genconf" to "1152 lipids" system as the method you mentioned. However, I still can't obtain a plain bilayer. I think the problem exisited after energy minimization. After energy minimization, the lipid molecules moved to the surface of the box, which might lead to a cylindric bilayer. What's your opinion?
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 4 months ago #1292
by djurre
Replied by djurre on topic Something about bilayer spontaneous-assembly
Does your bilayer look normal at the start of the simulation? Does your topology file have the right order (maybe past it here)? If your first system consisted of 100 water and 100 DPPC molecules, and you copy it four times (-nbox 2 2 1), the top file of your new system should be:
100 W
100 DPPC
100 W
100 DPPC
100 W
100 DPPC
100 W
100 DPPC
and should NOT look like:
400 W
400 DPPC
100 W
100 DPPC
100 W
100 DPPC
100 W
100 DPPC
100 W
100 DPPC
and should NOT look like:
400 W
400 DPPC
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 4 months ago #1296
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear Djurre,
I sent three pictures: "image after -nbox 3 3 1", "image after energy minimization", "image after MD for 90ns" to your email box and hope you could help me check the question.
Thanks a lot for your help.
I sent three pictures: "image after -nbox 3 3 1", "image after energy minimization", "image after MD for 90ns" to your email box and hope you could help me check the question.
Thanks a lot for your help.
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 4 months ago #1297
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear Djurre,
I have sent these files to your email box. Thanks again!
I have sent these files to your email box. Thanks again!
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 4 months ago #1298
by djurre
Replied by djurre on topic Something about bilayer spontaneous-assembly
Thanks for the files.
As I wrote in my previous post, your .top files has the wrong order. If you look in your starting.gro there are first 128 DPPC molecules, then comes W and then again 128 DPPC molecules, etc. However, in your top file you start with all the DPPC (1152) and then all the W. That is wrong. Read my last post again and change it.
As I wrote in my previous post, your .top files has the wrong order. If you look in your starting.gro there are first 128 DPPC molecules, then comes W and then again 128 DPPC molecules, etc. However, in your top file you start with all the DPPC (1152) and then all the W. That is wrong. Read my last post again and change it.
Please Log in or Create an account to join the conversation.
- Ray
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
11 years 4 months ago #1305
by Ray
Replied by Ray on topic Something about bilayer spontaneous-assembly
Dear Djurre,
Yes, it is the mistake in the top file.I was so careless about your suggestion in your last post. And again, I'm very grateful for your time and kind help!
Best,
Ray
Yes, it is the mistake in the top file.I was so careless about your suggestion in your last post. And again, I'm very grateful for your time and kind help!
Best,
Ray
Please Log in or Create an account to join the conversation.
Time to create page: 0.121 seconds