- Posts: 30
angle parameter
- msaeedi
-
Topic Author
- Offline
- Junior Boarder
Less
More
10 years 7 months ago #1923
by msaeedi
angle parameter was created by msaeedi
Hi, I have a question about angle parameter in cg topology.
I had an AA simulation and prepared bonded parameter for cg topology. After cg simulation, the angles changed unexpectedly. For example, I choose 110 degree with 25 kj/mol force constant and after cg simulation it changed to 35 degree. Should I change force constant to reach to corresponding AA angle?
For other bonded parameter such as bonds, should I do this procedure?
I had an AA simulation and prepared bonded parameter for cg topology. After cg simulation, the angles changed unexpectedly. For example, I choose 110 degree with 25 kj/mol force constant and after cg simulation it changed to 35 degree. Should I change force constant to reach to corresponding AA angle?
For other bonded parameter such as bonds, should I do this procedure?
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
10 years 7 months ago #1938
by djurre
Replied by djurre on topic angle parameter
Choosing a larger force constant might be a solution. However, it is better to start by figuring out what the problem is: eg is there an interactions with another, distant bead that forces the angle to be something different? Maybe you can exclude the interactions with that bead? That will most likely lead to more stable simulations in the end.
Please Log in or Create an account to join the conversation.
- msaeedi
-
Topic Author
- Offline
- Junior Boarder
Less
More
- Posts: 30
10 years 7 months ago - 10 years 7 months ago #1966
by msaeedi
Replied by msaeedi on topic angle parameter
Hi, thanks for your response and good advice.
My molecule is just like cholesterol and has 12 beads. I studied this itp and used this exclusion part in my topology:
[exclusions]
1 2 3 4 5 6 7 8 9 10 11 12
2 3 4 5 6 7 8 9 10 11 12
3 4 5 6 7 8 9 10 11 12
4 5 6 7 8 9 10 11 12
5 6 7 8 9 10 11 12
6 7 8 9 10 11 12
7 8 9 10 11 12
8 9 10 11 12
9 10 11 12
10 11 12
11 12
When I run this, I received this error:
There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 4.45968 nm
Change the number of nodes or mdrun option –rdd
And when I choose –rdd 1.4 the error repeated again.
Please help me to solve this. Thanks.
My molecule is just like cholesterol and has 12 beads. I studied this itp and used this exclusion part in my topology:
[exclusions]
1 2 3 4 5 6 7 8 9 10 11 12
2 3 4 5 6 7 8 9 10 11 12
3 4 5 6 7 8 9 10 11 12
4 5 6 7 8 9 10 11 12
5 6 7 8 9 10 11 12
6 7 8 9 10 11 12
7 8 9 10 11 12
8 9 10 11 12
9 10 11 12
10 11 12
11 12
When I run this, I received this error:
There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 4.45968 nm
Change the number of nodes or mdrun option –rdd
And when I choose –rdd 1.4 the error repeated again.
Please help me to solve this. Thanks.
Last edit: 10 years 7 months ago by msaeedi.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
10 years 7 months ago #1970
by djurre
Replied by djurre on topic angle parameter
Is it just like or exactly like cholesterol? Can there been any bonds/constraints that are very long?
Please Log in or Create an account to join the conversation.
- msaeedi
-
Topic Author
- Offline
- Junior Boarder
Less
More
- Posts: 30
10 years 7 months ago - 10 years 7 months ago #1971
by msaeedi
Replied by msaeedi on topic angle parameter
thanks for your response.
no it is simillar to the chol.
no it is simillar to the chol.
Last edit: 10 years 7 months ago by msaeedi.
Please Log in or Create an account to join the conversation.
- jaakko
-
- Offline
- Admin
Less
More
- Posts: 70
10 years 7 months ago - 10 years 7 months ago #2100
by jaakko
Replied by jaakko on topic angle parameter
Hi msaeedi,
if it's only similar to chol it would help to see the full itp file. You should also check that your initial configuration is realistic by, e.g., visualizing the molecule with VMD (look for abnormally long bonds etc.)
if it's only similar to chol it would help to see the full itp file. You should also check that your initial configuration is realistic by, e.g., visualizing the molecule with VMD (look for abnormally long bonds etc.)
Last edit: 10 years 7 months ago by jaakko.
Please Log in or Create an account to join the conversation.
Time to create page: 0.098 seconds