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heating failed
- syahidah
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11 years 1 week ago - 11 years 1 week ago #1511
by syahidah
heating failed was created by syahidah
Dear all,
thanks for all the replies before as i manage to solve most of my problems..
now i'm coarse-graining a new molecules, cremophor EL. the molecular structure is quite similar with PEG,PEO but the difference is it has 3 chains like triglycerol. i mange to do mapping and energy minimization, but when i want to proceed to heating, the "segmentation fault core dumped" keep happening after 600 steps.
attached here the files i use for the run:
cremophor.itp:
[moleculetype]
energy minimization:
heat.mdp:
your reply is greatly appreciated..
Thank you..
cheers,
MS
thanks for all the replies before as i manage to solve most of my problems..
now i'm coarse-graining a new molecules, cremophor EL. the molecular structure is quite similar with PEG,PEO but the difference is it has 3 chains like triglycerol. i mange to do mapping and energy minimization, but when i want to proceed to heating, the "segmentation fault core dumped" keep happening after 600 steps.
attached here the files i use for the run:
cremophor.itp:
[moleculetype]
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
;name exclusions
CMP 1
[atoms]
1 SN0 1 CMP COC 1 0.000 ;
2 SN0 1 CMP COC 2 0.000 ;
3 SN0 1 CMP COC 3 0.000 ;
4 SN0 1 CMP COC 4 0.000 ;
5 SN0 1 CMP COC 5 0.000 ;
6 SN0 1 CMP COC 6 0.000 ;
7 SN0 1 CMP COC 7 0.000 ;
8 SN0 1 CMP COC 8 0.000 ;
9 SN0 1 CMP COC 9 0.000 ;
10 SN0 1 CMP COC 10 0.000 ;
11 SN0 1 CMP COC 11 0.000 ;
12 SN0 1 CMP COC 12 0.000 ;
13 Na 1 CMP Na 13 0.000 ;
14 N0 1 CMP N0 14 0.000 ;
15 C1 1 CMP C1A 15 0.000 ;
16 C3 1 CMP C32 16 0.000 ;
17 P2 1 CMP P2 17 0.000 ;
18 C2 1 CMP C2A 18 0.000 ;
19 C2 1 CMP C2A 19 0.000 ;
20 SN0 1 CMP COC 20 0.000 ;
21 SN0 1 CMP COC 21 0.000 ;
22 SN0 1 CMP COC 22 0.000 ;
23 SN0 1 CMP COC 23 0.000 ;
24 SN0 1 CMP COC 24 0.000 ;
25 SN0 1 CMP COC 25 0.000 ;
26 SN0 1 CMP COC 26 0.000 ;
27 SN0 1 CMP COC 27 0.000 ;
28 SN0 1 CMP COC 28 0.000 ;
29 SN0 1 CMP COC 29 0.000 ;
30 SN0 1 CMP COC 30 0.000 ;
31 SN0 1 CMP COC 31 0.000 ;
32 Na 1 CMP Na 32 0.000 ;
33 N0 1 CMP N0 33 0.000 ;
34 C1 1 CMP C1B 34 0.000 ;
35 C3 1 CMP C32 35 0.000 ;
36 P2 1 CMP P2 36 0.000 ;
37 C2 1 CMP C2B 37 0.000 ;
38 C2 1 CMP C2B 38 0.000 ;
39 SN0 1 CMP COC 39 0.000 ;
40 SN0 1 CMP COC 40 0.000 ;
41 SN0 1 CMP COC 41 0.000 ;
42 SN0 1 CMP COC 42 0.000 ;
43 SN0 1 CMP COC 43 0.000 ;
44 SN0 1 CMP COC 44 0.000 ;
45 SN0 1 CMP COC 45 0.000 ;
46 SN0 1 CMP COC 46 0.000 ;
47 SN0 1 CMP COC 47 0.000 ;
48 SN0 1 CMP COC 48 0.000 ;
49 SN0 1 CMP COC 49 0.000 ;
50 Na 1 CMP Na 50 0.000 ;
51 N0 1 CMP N0 51 0.000 ;
52 C1 1 CMP C1C 52 0.000 ;
53 C3 1 CMP C32 53 0.000 ;
54 P2 1 CMP P2 54 0.000 ;
55 C2 1 CMP C2C 55 0.000 ;
56 C2 1 CMP C2C 56 0.000 ;
[ bonds ]
;backbonebackbone bonds
1 2 1 0.330 17000 ;
2 3 1 0.330 17000 ;
3 4 1 0.330 17000 ;
4 5 1 0.330 17000 ;
5 6 1 0.330 17000 ;
6 7 1 0.330 17000 ;
7 8 1 0.330 17000 ;
8 9 1 0.330 17000 ;
9 10 1 0.330 17000 ;
10 11 1 0.330 17000 ;
11 12 1 0.330 17000 ;
12 13 1 0.330 17000 ;
13 14 1 0.430 1250 ;
14 15 1 0.430 1250 ;
15 16 1 0.430 1250 ;
16 17 1 0.430 1250 ;
17 18 1 0.430 1250 ;
18 19 1 0.430 1250 ;
20 21 1 0.330 17000 ;
21 22 1 0.330 17000 ;
22 23 1 0.330 17000 ;
23 24 1 0.330 17000 ;
24 25 1 0.330 17000 ;
25 26 1 0.330 17000 ;
26 27 1 0.330 17000 ;
27 28 1 0.330 17000 ;
28 29 1 0.330 17000 ;
29 30 1 0.330 17000 ;
30 31 1 0.330 17000 ;
31 32 1 0.330 17000 ;
32 33 1 0.430 1250 ;
33 34 1 0.430 1250 ;
34 35 1 0.430 1250 ;
35 36 1 0.430 1250 ;
36 37 1 0.430 1250 ;
37 38 1 0.430 1250 ;
39 40 1 0.330 17000 ;
40 41 1 0.330 17000 ;
41 42 1 0.330 17000 ;
42 43 1 0.330 17000 ;
43 44 1 0.330 17000 ;
44 45 1 0.330 17000 ;
45 46 1 0.330 17000 ;
46 47 1 0.330 17000 ;
47 48 1 0.330 17000 ;
48 49 1 0.330 17000 ;
49 50 1 0.330 17000 ;
50 51 1 0.430 1250 ;
51 52 1 0.430 1250 ;
52 53 1 0.430 1250 ;
53 54 1 0.430 1250 ;
54 55 1 0.430 1250 ;
55 56 1 0.430 1250 ;
1 20 1 0.430 1250 ;
20 39 1 0.430 1250 ;
[angles]
;backbonebackbonebackbone angles
;
; Note: in the original publication a force constant of 85 was used with a cosine-type angle potential (type 2).
; Numerical stability is improved when a normal harmonic angle potential (type 1) is used with a force constant of 50.
; The two potentials are virtually identical around the equilibrium angle, but the probability density of
; angles around 180 degrees is lowered avoiding problems with the dihedral angles becoming ill-defined.
;
1 2 3 1 130.00 85 ;
2 3 4 1 130.00 85 ;
3 4 5 1 130.00 85 ;
4 5 6 1 130.00 85 ;
5 6 7 1 130.00 85 ;
6 7 8 1 130.00 85 ;
7 8 9 1 130.00 85 ;
8 9 10 1 130.00 85 ;
9 10 11 1 130.00 85 ;
10 11 12 1 130.00 85 ;
11 12 13 1 130.00 85 ;
12 13 14 1 180.00 25 ;
13 14 15 1 180.00 25 ;
14 15 16 1 180.00 25 ;
15 16 17 1 120.00 45 ;
16 17 18 1 180.00 25 ;
17 18 19 1 180.00 25 ;
20 21 22 1 130.00 25 ;
21 22 23 1 130.00 25 ;
22 23 24 1 130.00 25 ;
23 24 25 1 130.00 25 ;
24 25 26 1 130.00 25 ;
25 26 27 1 130.00 25 ;
26 27 28 1 130.00 25 ;
27 28 29 1 130.00 50 ;
28 29 30 1 130.00 50 ;
31 32 33 1 180.00 50 ;
32 33 34 1 180.00 50 ;
33 34 35 1 180.00 50 ;
34 35 36 1 120.00 45 ;
35 36 37 1 180.00 50 ;
36 37 38 1 180.00 50 ;
39 40 41 1 180.00 50 ;
40 41 42 1 180.00 50 ;
41 42 43 1 180.00 50 ;
42 43 44 1 180.00 50 ;
43 44 45 1 180.00 50 ;
44 45 46 1 180.00 50 ;
45 46 47 1 180.00 50 ;
46 47 48 1 180.00 50 ;
47 48 49 1 180.00 50 ;
48 49 50 1 180.00 50 ;
49 50 51 1 180.00 50 ;
50 51 52 1 180.00 50 ;
51 52 53 1 180.00 50 ;
52 53 54 1 120.00 45 ;
53 54 55 1 180.00 50 ;
54 55 56 1 180.00 50 ;
1 20 39 1 130.00 25 ;
[dihedrals]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
2 3 4 5 1 180.00 1.96 1
2 3 4 5 1 0 0.18 2
2 3 4 5 1 0 0.33 3
2 3 4 5 1 0 0.12 4
3 4 5 6 1 180.00 1.96 1
3 4 5 6 1 0 0.18 2
3 4 5 6 1 0 0.33 3
3 4 5 6 1 0 0.12 4
4 5 6 7 1 180.00 1.96 1
4 5 6 7 1 0 0.18 2
4 5 6 7 1 0 0.33 3
4 5 6 7 1 0 0.12 4
5 6 7 8 1 180.00 1.96 1
5 6 7 8 1 0 0.18 2
5 6 7 8 1 0 0.33 3
5 6 7 8 1 0 0.12 4
6 7 8 9 1 180.00 1.96 1
6 7 8 9 1 0 0.18 2
6 7 8 9 1 0 0.33 3
6 7 8 9 1 0 0.12 4
7 8 9 10 1 180.00 1.96 1
7 8 9 10 1 0 0.18 2
7 8 9 10 1 0 0.33 3
7 8 9 10 1 0 0.12 4
8 9 10 11 1 180.00 1.96 1
8 9 10 11 1 0 0.18 2
8 9 10 11 1 0 0.33 3
8 9 10 11 1 0 0.12 4
9 10 11 12 1 180.00 1.96 1
9 10 11 12 1 0 0.18 2
9 10 11 12 1 0 0.33 3
9 10 11 12 1 0 0.12 4
20 21 22 23 1 180.00 1.96 1
20 21 22 23 1 0 0.18 2
20 21 22 23 1 0 0.33 3
20 21 22 23 1 0 0.12 4
21 22 23 24 1 180.00 1.96 1
21 22 23 24 1 0 0.18 2
21 22 23 24 1 0 0.33 3
21 22 23 24 1 0 0.12 4
22 23 24 25 1 180.00 1.96 1
22 23 24 25 1 0 0.18 2
22 23 24 25 1 0 0.33 3
22 23 24 25 1 0 0.12 4
23 24 25 26 1 180.00 1.96 1
23 24 25 26 1 0 0.18 2
23 24 25 26 1 0 0.33 3
23 24 25 26 1 0 0.12 4
24 25 26 27 1 180.00 1.96 1
24 25 26 27 1 0 0.18 2
24 25 26 27 1 0 0.33 3
24 25 26 27 1 0 0.12 4
25 26 27 28 1 180.00 1.96 1
25 26 27 28 1 0 0.18 2
25 26 27 28 1 0 0.33 3
25 26 27 28 1 0 0.12 4
26 27 28 29 1 180.00 1.96 1
26 27 28 29 1 0 0.18 2
26 27 28 29 1 0 0.33 3
26 27 28 29 1 0 0.12 4
27 28 29 30 1 180.00 1.96 1
27 28 29 30 1 0 0.18 2
27 28 29 30 1 0 0.33 3
27 28 29 30 1 0 0.12 4
28 29 30 31 1 180.00 1.96 1
28 29 30 31 1 0 0.18 2
28 29 30 31 1 0 0.33 3
28 29 30 31 1 0 0.12 4
39 40 41 42 1 180.00 1.96 1
39 40 41 42 1 0 0.18 2
39 40 41 42 1 0 0.33 3
39 40 41 42 1 0 0.12 4
40 41 42 43 1 180.00 1.96 1
40 41 42 43 1 0 0.18 2
40 41 42 43 1 0 0.33 3
40 41 42 43 1 0 0.12 4
41 42 43 44 1 180.00 1.96 1
41 42 43 44 1 0 0.18 2
41 42 43 44 1 0 0.33 3
41 42 43 44 1 0 0.12 4
42 43 44 45 1 180.00 1.96 1
42 43 44 45 1 0 0.18 2
42 43 44 45 1 0 0.33 3
42 43 44 45 1 0 0.12 4
43 44 45 46 1 180.00 1.96 1
43 44 45 46 1 0 0.18 2
43 44 45 46 1 0 0.33 3
43 44 45 46 1 0 0.12 4
44 45 46 47 1 180.00 1.96 1
44 45 46 47 1 0 0.18 2
44 45 46 47 1 0 0.33 3
44 45 46 47 1 0 0.12 4
45 46 47 48 1 180.00 1.96 1
45 46 47 48 1 0 0.18 2
45 46 47 48 1 0 0.33 3
45 46 47 48 1 0 0.12 4
46 47 48 49 1 180.00 1.96 1
46 47 48 49 1 0 0.18 2
46 47 48 49 1 0 0.33 3
46 47 48 49 1 0 0.12 4
1 20 39 40 1 180.00 1.96 1
1 20 39 40 1 0 0.18 2
1 20 39 40 1 0 0.33 3
1 20 39 40 1 0 0.12 4
CMP 1
[atoms]
1 SN0 1 CMP COC 1 0.000 ;
2 SN0 1 CMP COC 2 0.000 ;
3 SN0 1 CMP COC 3 0.000 ;
4 SN0 1 CMP COC 4 0.000 ;
5 SN0 1 CMP COC 5 0.000 ;
6 SN0 1 CMP COC 6 0.000 ;
7 SN0 1 CMP COC 7 0.000 ;
8 SN0 1 CMP COC 8 0.000 ;
9 SN0 1 CMP COC 9 0.000 ;
10 SN0 1 CMP COC 10 0.000 ;
11 SN0 1 CMP COC 11 0.000 ;
12 SN0 1 CMP COC 12 0.000 ;
13 Na 1 CMP Na 13 0.000 ;
14 N0 1 CMP N0 14 0.000 ;
15 C1 1 CMP C1A 15 0.000 ;
16 C3 1 CMP C32 16 0.000 ;
17 P2 1 CMP P2 17 0.000 ;
18 C2 1 CMP C2A 18 0.000 ;
19 C2 1 CMP C2A 19 0.000 ;
20 SN0 1 CMP COC 20 0.000 ;
21 SN0 1 CMP COC 21 0.000 ;
22 SN0 1 CMP COC 22 0.000 ;
23 SN0 1 CMP COC 23 0.000 ;
24 SN0 1 CMP COC 24 0.000 ;
25 SN0 1 CMP COC 25 0.000 ;
26 SN0 1 CMP COC 26 0.000 ;
27 SN0 1 CMP COC 27 0.000 ;
28 SN0 1 CMP COC 28 0.000 ;
29 SN0 1 CMP COC 29 0.000 ;
30 SN0 1 CMP COC 30 0.000 ;
31 SN0 1 CMP COC 31 0.000 ;
32 Na 1 CMP Na 32 0.000 ;
33 N0 1 CMP N0 33 0.000 ;
34 C1 1 CMP C1B 34 0.000 ;
35 C3 1 CMP C32 35 0.000 ;
36 P2 1 CMP P2 36 0.000 ;
37 C2 1 CMP C2B 37 0.000 ;
38 C2 1 CMP C2B 38 0.000 ;
39 SN0 1 CMP COC 39 0.000 ;
40 SN0 1 CMP COC 40 0.000 ;
41 SN0 1 CMP COC 41 0.000 ;
42 SN0 1 CMP COC 42 0.000 ;
43 SN0 1 CMP COC 43 0.000 ;
44 SN0 1 CMP COC 44 0.000 ;
45 SN0 1 CMP COC 45 0.000 ;
46 SN0 1 CMP COC 46 0.000 ;
47 SN0 1 CMP COC 47 0.000 ;
48 SN0 1 CMP COC 48 0.000 ;
49 SN0 1 CMP COC 49 0.000 ;
50 Na 1 CMP Na 50 0.000 ;
51 N0 1 CMP N0 51 0.000 ;
52 C1 1 CMP C1C 52 0.000 ;
53 C3 1 CMP C32 53 0.000 ;
54 P2 1 CMP P2 54 0.000 ;
55 C2 1 CMP C2C 55 0.000 ;
56 C2 1 CMP C2C 56 0.000 ;
[ bonds ]
;backbonebackbone bonds
1 2 1 0.330 17000 ;
2 3 1 0.330 17000 ;
3 4 1 0.330 17000 ;
4 5 1 0.330 17000 ;
5 6 1 0.330 17000 ;
6 7 1 0.330 17000 ;
7 8 1 0.330 17000 ;
8 9 1 0.330 17000 ;
9 10 1 0.330 17000 ;
10 11 1 0.330 17000 ;
11 12 1 0.330 17000 ;
12 13 1 0.330 17000 ;
13 14 1 0.430 1250 ;
14 15 1 0.430 1250 ;
15 16 1 0.430 1250 ;
16 17 1 0.430 1250 ;
17 18 1 0.430 1250 ;
18 19 1 0.430 1250 ;
20 21 1 0.330 17000 ;
21 22 1 0.330 17000 ;
22 23 1 0.330 17000 ;
23 24 1 0.330 17000 ;
24 25 1 0.330 17000 ;
25 26 1 0.330 17000 ;
26 27 1 0.330 17000 ;
27 28 1 0.330 17000 ;
28 29 1 0.330 17000 ;
29 30 1 0.330 17000 ;
30 31 1 0.330 17000 ;
31 32 1 0.330 17000 ;
32 33 1 0.430 1250 ;
33 34 1 0.430 1250 ;
34 35 1 0.430 1250 ;
35 36 1 0.430 1250 ;
36 37 1 0.430 1250 ;
37 38 1 0.430 1250 ;
39 40 1 0.330 17000 ;
40 41 1 0.330 17000 ;
41 42 1 0.330 17000 ;
42 43 1 0.330 17000 ;
43 44 1 0.330 17000 ;
44 45 1 0.330 17000 ;
45 46 1 0.330 17000 ;
46 47 1 0.330 17000 ;
47 48 1 0.330 17000 ;
48 49 1 0.330 17000 ;
49 50 1 0.330 17000 ;
50 51 1 0.430 1250 ;
51 52 1 0.430 1250 ;
52 53 1 0.430 1250 ;
53 54 1 0.430 1250 ;
54 55 1 0.430 1250 ;
55 56 1 0.430 1250 ;
1 20 1 0.430 1250 ;
20 39 1 0.430 1250 ;
[angles]
;backbonebackbonebackbone angles
;
; Note: in the original publication a force constant of 85 was used with a cosine-type angle potential (type 2).
; Numerical stability is improved when a normal harmonic angle potential (type 1) is used with a force constant of 50.
; The two potentials are virtually identical around the equilibrium angle, but the probability density of
; angles around 180 degrees is lowered avoiding problems with the dihedral angles becoming ill-defined.
;
1 2 3 1 130.00 85 ;
2 3 4 1 130.00 85 ;
3 4 5 1 130.00 85 ;
4 5 6 1 130.00 85 ;
5 6 7 1 130.00 85 ;
6 7 8 1 130.00 85 ;
7 8 9 1 130.00 85 ;
8 9 10 1 130.00 85 ;
9 10 11 1 130.00 85 ;
10 11 12 1 130.00 85 ;
11 12 13 1 130.00 85 ;
12 13 14 1 180.00 25 ;
13 14 15 1 180.00 25 ;
14 15 16 1 180.00 25 ;
15 16 17 1 120.00 45 ;
16 17 18 1 180.00 25 ;
17 18 19 1 180.00 25 ;
20 21 22 1 130.00 25 ;
21 22 23 1 130.00 25 ;
22 23 24 1 130.00 25 ;
23 24 25 1 130.00 25 ;
24 25 26 1 130.00 25 ;
25 26 27 1 130.00 25 ;
26 27 28 1 130.00 25 ;
27 28 29 1 130.00 50 ;
28 29 30 1 130.00 50 ;
31 32 33 1 180.00 50 ;
32 33 34 1 180.00 50 ;
33 34 35 1 180.00 50 ;
34 35 36 1 120.00 45 ;
35 36 37 1 180.00 50 ;
36 37 38 1 180.00 50 ;
39 40 41 1 180.00 50 ;
40 41 42 1 180.00 50 ;
41 42 43 1 180.00 50 ;
42 43 44 1 180.00 50 ;
43 44 45 1 180.00 50 ;
44 45 46 1 180.00 50 ;
45 46 47 1 180.00 50 ;
46 47 48 1 180.00 50 ;
47 48 49 1 180.00 50 ;
48 49 50 1 180.00 50 ;
49 50 51 1 180.00 50 ;
50 51 52 1 180.00 50 ;
51 52 53 1 180.00 50 ;
52 53 54 1 120.00 45 ;
53 54 55 1 180.00 50 ;
54 55 56 1 180.00 50 ;
1 20 39 1 130.00 25 ;
[dihedrals]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
2 3 4 5 1 180.00 1.96 1
2 3 4 5 1 0 0.18 2
2 3 4 5 1 0 0.33 3
2 3 4 5 1 0 0.12 4
3 4 5 6 1 180.00 1.96 1
3 4 5 6 1 0 0.18 2
3 4 5 6 1 0 0.33 3
3 4 5 6 1 0 0.12 4
4 5 6 7 1 180.00 1.96 1
4 5 6 7 1 0 0.18 2
4 5 6 7 1 0 0.33 3
4 5 6 7 1 0 0.12 4
5 6 7 8 1 180.00 1.96 1
5 6 7 8 1 0 0.18 2
5 6 7 8 1 0 0.33 3
5 6 7 8 1 0 0.12 4
6 7 8 9 1 180.00 1.96 1
6 7 8 9 1 0 0.18 2
6 7 8 9 1 0 0.33 3
6 7 8 9 1 0 0.12 4
7 8 9 10 1 180.00 1.96 1
7 8 9 10 1 0 0.18 2
7 8 9 10 1 0 0.33 3
7 8 9 10 1 0 0.12 4
8 9 10 11 1 180.00 1.96 1
8 9 10 11 1 0 0.18 2
8 9 10 11 1 0 0.33 3
8 9 10 11 1 0 0.12 4
9 10 11 12 1 180.00 1.96 1
9 10 11 12 1 0 0.18 2
9 10 11 12 1 0 0.33 3
9 10 11 12 1 0 0.12 4
20 21 22 23 1 180.00 1.96 1
20 21 22 23 1 0 0.18 2
20 21 22 23 1 0 0.33 3
20 21 22 23 1 0 0.12 4
21 22 23 24 1 180.00 1.96 1
21 22 23 24 1 0 0.18 2
21 22 23 24 1 0 0.33 3
21 22 23 24 1 0 0.12 4
22 23 24 25 1 180.00 1.96 1
22 23 24 25 1 0 0.18 2
22 23 24 25 1 0 0.33 3
22 23 24 25 1 0 0.12 4
23 24 25 26 1 180.00 1.96 1
23 24 25 26 1 0 0.18 2
23 24 25 26 1 0 0.33 3
23 24 25 26 1 0 0.12 4
24 25 26 27 1 180.00 1.96 1
24 25 26 27 1 0 0.18 2
24 25 26 27 1 0 0.33 3
24 25 26 27 1 0 0.12 4
25 26 27 28 1 180.00 1.96 1
25 26 27 28 1 0 0.18 2
25 26 27 28 1 0 0.33 3
25 26 27 28 1 0 0.12 4
26 27 28 29 1 180.00 1.96 1
26 27 28 29 1 0 0.18 2
26 27 28 29 1 0 0.33 3
26 27 28 29 1 0 0.12 4
27 28 29 30 1 180.00 1.96 1
27 28 29 30 1 0 0.18 2
27 28 29 30 1 0 0.33 3
27 28 29 30 1 0 0.12 4
28 29 30 31 1 180.00 1.96 1
28 29 30 31 1 0 0.18 2
28 29 30 31 1 0 0.33 3
28 29 30 31 1 0 0.12 4
39 40 41 42 1 180.00 1.96 1
39 40 41 42 1 0 0.18 2
39 40 41 42 1 0 0.33 3
39 40 41 42 1 0 0.12 4
40 41 42 43 1 180.00 1.96 1
40 41 42 43 1 0 0.18 2
40 41 42 43 1 0 0.33 3
40 41 42 43 1 0 0.12 4
41 42 43 44 1 180.00 1.96 1
41 42 43 44 1 0 0.18 2
41 42 43 44 1 0 0.33 3
41 42 43 44 1 0 0.12 4
42 43 44 45 1 180.00 1.96 1
42 43 44 45 1 0 0.18 2
42 43 44 45 1 0 0.33 3
42 43 44 45 1 0 0.12 4
43 44 45 46 1 180.00 1.96 1
43 44 45 46 1 0 0.18 2
43 44 45 46 1 0 0.33 3
43 44 45 46 1 0 0.12 4
44 45 46 47 1 180.00 1.96 1
44 45 46 47 1 0 0.18 2
44 45 46 47 1 0 0.33 3
44 45 46 47 1 0 0.12 4
45 46 47 48 1 180.00 1.96 1
45 46 47 48 1 0 0.18 2
45 46 47 48 1 0 0.33 3
45 46 47 48 1 0 0.12 4
46 47 48 49 1 180.00 1.96 1
46 47 48 49 1 0 0.18 2
46 47 48 49 1 0 0.33 3
46 47 48 49 1 0 0.12 4
1 20 39 40 1 180.00 1.96 1
1 20 39 40 1 0 0.18 2
1 20 39 40 1 0 0.33 3
1 20 39 40 1 0 0.12 4
energy minimization:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = steep
; start time and timestep in ps
tinit = 0.0
dt = 0.025
nsteps = 1000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
emtol = 30
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = no
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 298
gen_seed = -1
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = steep
; start time and timestep in ps
tinit = 0.0
dt = 0.025
nsteps = 1000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
emtol = 30
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = no
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 298
gen_seed = -1
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
heat.mdp:
Warning: Spoiler!
[ Click to expand ]
[ Click to hide ]
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = md
; start time and timestep in ps
tinit = 0.0
dt = 0.04
nsteps = 250000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = CMP W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = CMP W
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = CMP W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 298 298
; Pressure coupling =
Pcoupl = no
;Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
;tau_p = 1.0
;compressibility = 5e-6
;ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 105
gen_seed = -1
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = md
; start time and timestep in ps
tinit = 0.0
dt = 0.04
nsteps = 250000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps = CMP W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = CMP W
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = CMP W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 298 298
; Pressure coupling =
Pcoupl = no
;Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
;tau_p = 1.0
;compressibility = 5e-6
;ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 105
gen_seed = -1
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
your reply is greatly appreciated..
Thank you..
cheers,
MS
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- djurre
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11 years 1 week ago #1514
by djurre
Replied by djurre on topic heating failed
What might be a problem is the timestep during you heating. You use 40 fs. For many molecules this is to much (for example proteins only run at 20fs), this will be probably true for you molecules (there are some pretty high force constants). As a first short simulation after EM you might even want to go back to +/-5 fs to get things relaxed.
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11 years 1 week ago #1515
by syahidah
Replied by syahidah on topic heating failed
million thanks Djurre!managed to solve that!
so, meaning that,in equilibration run i can increase it to 20-40fs (as stated in example.mdp)?
so, meaning that,in equilibration run i can increase it to 20-40fs (as stated in example.mdp)?
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11 years 1 week ago #1531
by syahidah
Replied by syahidah on topic heating failed
Hi Djurre,
now i managed to complete eq stage where i used timestep = 10 fs
however, when i analysed SASA for this eq xtc file, i got all 0 for the hydrophilic values.
is it the problem came from the mdp? or itp?
Thank you..
now i managed to complete eq stage where i used timestep = 10 fs
however, when i analysed SASA for this eq xtc file, i got all 0 for the hydrophilic values.
is it the problem came from the mdp? or itp?
Thank you..
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11 years 1 week ago #1532
by djurre
Replied by djurre on topic heating failed
I don't know how hydrophobic/hydrophylic is defined by g_sasa, but it might be that this is done by atom names in a file somewhere. In that case g_sasa just doesn't recognize Martini beads as being hydrophyllic.
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- syahidah
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11 years 6 days ago #1537
by syahidah
Replied by syahidah on topic heating failed
Hi Djurre,
i completed equilibration part, however with 10fs time step, my production run crashed in the middle of run..as stated in .mdp file in the homepage, smaller than 20fs is not recomended. so, is is okay if i use smaller than 10fs?
for the g-sas, doe it mean my coarse-graing part is wrong?
best,
MS
i completed equilibration part, however with 10fs time step, my production run crashed in the middle of run..as stated in .mdp file in the homepage, smaller than 20fs is not recomended. so, is is okay if i use smaller than 10fs?
for the g-sas, doe it mean my coarse-graing part is wrong?
best,
MS
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11 years 6 days ago #1538
by djurre
Replied by djurre on topic heating failed
10fs is not wrong, it is just a pity you are wasting so much computer time by using a small timestep. You might want to try and find out WHY the simulations crashes: which molecules are the first to crash and which bond/angle is the reason. If you find that out, you can tune them further.
I don't think anything is wrong about g_sas. The parameters you are feeding to it might not be correct for CG.
I don't think anything is wrong about g_sas. The parameters you are feeding to it might not be correct for CG.
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