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Parametrizing new molecule with backward.py
- Tomasz
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9 years 8 months ago #4058
by Tomasz
Parametrizing new molecule with backward.py was created by Tomasz
Hi,
I wanted to parametrize DPPC molecule using backward method (i.e. making atomistic simulation and later on transforming it to coarse grained model). Unfortunately, I have problems with backward.py:
python backward.py -f test793.gro -o out793.gro -from gromos -to martini
One of the beads is escaping from molecule (i.e. it is far from molecule). Below I am attaching all files, but the most important part is 5 atoms from atomistic simulation:
1DPPC O12 40 1.377 2.787 2.394
1DPPC O11 41 1.598 2.870 2.262
1DPPC O14 42 1.533 2.979 2.486
1DPPC O13 43 1.612 2.731 2.494
1DPPC P 44 1.544 2.844 2.427
which are transformed by backward method to:
1DPPC R1 2 1.533 2.842 0.190
As you can see last coordinate of the bead (0.190) somehow escapes from all atoms within this bead (coordinate are in between (2.2,2.5)). I do not have idea why last of the coordinates is different. Am I making mistake?
With kind regards,
Tomasz
Map of the dppc: dppc.gromacs.map:
[ molecule ]
DPPC
[ martini ]
R0 R1 R2 R3 R4 R5 R6 R7 R8 R9 R10 R11
[ mapping ]
gromos
[ atoms ]
1 6C31 R7
2 5C31 R7
3 4C31 R7
4 3C31 R6 R7
5 2C31 R6
6 1C31 R6
7 0C31 R6
8 C39 R5
9 C36 R5
10 C38 R5
11 C37 R5
12 C35 R4
13 C34 R4
14 C33 R4
15 C32 R4
16 O32 R3
17 C31 R3
18 O31 R3
19 C3 R3
20 O21 R2
21 C2 R2
22 C1 R2
23 C22 R8
24 O22 R2
25 C21 R2
26 C23 R8
27 C26 R9
28 C25 R8
29 C24 R8
30 C28 R9
31 C27 R9
32 C29 R9
33 2C21 R10
34 1C21 R10
35 0C21 R10
36 4C21 R11
37 3C21 R10 R11
38 6C21 R11
39 5C21 R11
40 O12 R1
41 O11 R1
42 O14 R1
43 O13 R1
44 P R1
45 C11 R0
46 C12 R0
47 N R0
48 C13 R0
49 C14 R0
50 C15 R0
test0793.gro:
Generated by trjconv : DPPC in sol in water t= 793.00000
50
1DPPC 6C31 1 2.393 3.214 0.555
1DPPC 5C31 2 2.434 3.269 0.690
1DPPC 4C31 3 2.344 3.379 0.743
1DPPC 3C31 4 2.232 3.331 0.834
1DPPC 2C31 5 2.168 3.448 0.907
1DPPC 1C31 6 2.043 3.392 0.973
1DPPC 0C31 7 2.070 3.285 1.078
1DPPC C39 8 1.953 3.279 1.175
1DPPC C36 9 1.951 3.363 1.478
1DPPC C38 10 1.911 3.415 1.226
1DPPC C37 11 1.855 3.400 1.366
1DPPC C35 12 1.865 3.349 1.603
1DPPC C34 13 1.905 3.236 1.696
1DPPC C33 14 1.869 3.102 1.633
1DPPC C32 15 1.940 2.993 1.711
1DPPC O32 16 1.817 2.800 1.784
1DPPC C31 17 1.850 2.916 1.806
1DPPC O31 18 1.803 2.989 1.911
1DPPC C3 19 1.688 2.945 1.984
1DPPC O21 20 1.504 3.081 2.087
1DPPC C2 21 1.641 3.040 2.095
1DPPC C1 22 1.680 2.974 2.228
1DPPC C22 23 1.320 3.200 1.999
1DPPC O22 24 1.549 3.255 1.940
1DPPC C21 25 1.471 3.179 1.998
1DPPC C23 26 1.269 3.183 1.857
1DPPC C26 27 1.360 3.055 1.594
1DPPC C25 28 1.234 3.013 1.667
1DPPC C24 29 1.252 3.037 1.816
1DPPC C28 30 1.567 2.965 1.522
1DPPC C27 31 1.449 2.933 1.613
1DPPC C29 32 1.656 2.848 1.486
1DPPC 2C21 33 1.882 2.856 1.170
1DPPC 1C21 34 1.842 2.824 1.313
1DPPC 0C21 35 1.710 2.890 1.350
1DPPC 4C21 36 2.064 2.871 0.992
1DPPC 3C21 37 2.023 2.818 1.129
1DPPC 6C21 38 2.245 2.873 0.818
1DPPC 5C21 39 2.209 2.837 0.961
1DPPC O12 40 1.377 2.787 2.394
1DPPC O11 41 1.598 2.870 2.262
1DPPC O14 42 1.533 2.979 2.486
1DPPC O13 43 1.612 2.731 2.494
1DPPC P 44 1.544 2.844 2.427
1DPPC C11 45 1.305 2.867 2.312
1DPPC C12 46 1.270 2.783 2.189
1DPPC N 47 1.156 2.684 2.210
1DPPC C13 48 1.220 2.551 2.198
1DPPC C14 49 1.069 2.691 2.086
1DPPC C15 50 1.065 2.679 2.326
3.53645 3.83720 3.70475
out0793.gro
Mapped structure from gromos to MARTINI
12
1DPPC R0 1 1.181 2.709 2.220
1DPPC R1 2 1.533 2.842 0.190
1DPPC R2 3 1.569 3.106 2.070
1DPPC R3 4 1.789 2.912 1.871
1DPPC R4 5 1.895 3.170 1.661
1DPPC R5 6 1.917 3.364 1.311
1DPPC R6 7 2.128 3.364 0.948
1DPPC R7 8 2.351 3.298 0.706
1DPPC R8 9 1.269 3.108 1.835
1DPPC R9 10 1.508 2.950 1.554
1DPPC R10 11 1.864 2.847 1.240
1DPPC R11 12 2.135 2.850 0.975
3.53645 3.83720 3.70475 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
I wanted to parametrize DPPC molecule using backward method (i.e. making atomistic simulation and later on transforming it to coarse grained model). Unfortunately, I have problems with backward.py:
python backward.py -f test793.gro -o out793.gro -from gromos -to martini
One of the beads is escaping from molecule (i.e. it is far from molecule). Below I am attaching all files, but the most important part is 5 atoms from atomistic simulation:
1DPPC O12 40 1.377 2.787 2.394
1DPPC O11 41 1.598 2.870 2.262
1DPPC O14 42 1.533 2.979 2.486
1DPPC O13 43 1.612 2.731 2.494
1DPPC P 44 1.544 2.844 2.427
which are transformed by backward method to:
1DPPC R1 2 1.533 2.842 0.190
As you can see last coordinate of the bead (0.190) somehow escapes from all atoms within this bead (coordinate are in between (2.2,2.5)). I do not have idea why last of the coordinates is different. Am I making mistake?
With kind regards,
Tomasz
Map of the dppc: dppc.gromacs.map:
[ molecule ]
DPPC
[ martini ]
R0 R1 R2 R3 R4 R5 R6 R7 R8 R9 R10 R11
[ mapping ]
gromos
[ atoms ]
1 6C31 R7
2 5C31 R7
3 4C31 R7
4 3C31 R6 R7
5 2C31 R6
6 1C31 R6
7 0C31 R6
8 C39 R5
9 C36 R5
10 C38 R5
11 C37 R5
12 C35 R4
13 C34 R4
14 C33 R4
15 C32 R4
16 O32 R3
17 C31 R3
18 O31 R3
19 C3 R3
20 O21 R2
21 C2 R2
22 C1 R2
23 C22 R8
24 O22 R2
25 C21 R2
26 C23 R8
27 C26 R9
28 C25 R8
29 C24 R8
30 C28 R9
31 C27 R9
32 C29 R9
33 2C21 R10
34 1C21 R10
35 0C21 R10
36 4C21 R11
37 3C21 R10 R11
38 6C21 R11
39 5C21 R11
40 O12 R1
41 O11 R1
42 O14 R1
43 O13 R1
44 P R1
45 C11 R0
46 C12 R0
47 N R0
48 C13 R0
49 C14 R0
50 C15 R0
test0793.gro:
Generated by trjconv : DPPC in sol in water t= 793.00000
50
1DPPC 6C31 1 2.393 3.214 0.555
1DPPC 5C31 2 2.434 3.269 0.690
1DPPC 4C31 3 2.344 3.379 0.743
1DPPC 3C31 4 2.232 3.331 0.834
1DPPC 2C31 5 2.168 3.448 0.907
1DPPC 1C31 6 2.043 3.392 0.973
1DPPC 0C31 7 2.070 3.285 1.078
1DPPC C39 8 1.953 3.279 1.175
1DPPC C36 9 1.951 3.363 1.478
1DPPC C38 10 1.911 3.415 1.226
1DPPC C37 11 1.855 3.400 1.366
1DPPC C35 12 1.865 3.349 1.603
1DPPC C34 13 1.905 3.236 1.696
1DPPC C33 14 1.869 3.102 1.633
1DPPC C32 15 1.940 2.993 1.711
1DPPC O32 16 1.817 2.800 1.784
1DPPC C31 17 1.850 2.916 1.806
1DPPC O31 18 1.803 2.989 1.911
1DPPC C3 19 1.688 2.945 1.984
1DPPC O21 20 1.504 3.081 2.087
1DPPC C2 21 1.641 3.040 2.095
1DPPC C1 22 1.680 2.974 2.228
1DPPC C22 23 1.320 3.200 1.999
1DPPC O22 24 1.549 3.255 1.940
1DPPC C21 25 1.471 3.179 1.998
1DPPC C23 26 1.269 3.183 1.857
1DPPC C26 27 1.360 3.055 1.594
1DPPC C25 28 1.234 3.013 1.667
1DPPC C24 29 1.252 3.037 1.816
1DPPC C28 30 1.567 2.965 1.522
1DPPC C27 31 1.449 2.933 1.613
1DPPC C29 32 1.656 2.848 1.486
1DPPC 2C21 33 1.882 2.856 1.170
1DPPC 1C21 34 1.842 2.824 1.313
1DPPC 0C21 35 1.710 2.890 1.350
1DPPC 4C21 36 2.064 2.871 0.992
1DPPC 3C21 37 2.023 2.818 1.129
1DPPC 6C21 38 2.245 2.873 0.818
1DPPC 5C21 39 2.209 2.837 0.961
1DPPC O12 40 1.377 2.787 2.394
1DPPC O11 41 1.598 2.870 2.262
1DPPC O14 42 1.533 2.979 2.486
1DPPC O13 43 1.612 2.731 2.494
1DPPC P 44 1.544 2.844 2.427
1DPPC C11 45 1.305 2.867 2.312
1DPPC C12 46 1.270 2.783 2.189
1DPPC N 47 1.156 2.684 2.210
1DPPC C13 48 1.220 2.551 2.198
1DPPC C14 49 1.069 2.691 2.086
1DPPC C15 50 1.065 2.679 2.326
3.53645 3.83720 3.70475
out0793.gro
Mapped structure from gromos to MARTINI
12
1DPPC R0 1 1.181 2.709 2.220
1DPPC R1 2 1.533 2.842 0.190
1DPPC R2 3 1.569 3.106 2.070
1DPPC R3 4 1.789 2.912 1.871
1DPPC R4 5 1.895 3.170 1.661
1DPPC R5 6 1.917 3.364 1.311
1DPPC R6 7 2.128 3.364 0.948
1DPPC R7 8 2.351 3.298 0.706
1DPPC R8 9 1.269 3.108 1.835
1DPPC R9 10 1.508 2.950 1.554
1DPPC R10 11 1.864 2.847 1.240
1DPPC R11 12 2.135 2.850 0.975
3.53645 3.83720 3.70475 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
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- xavier
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- Posts: 416
9 years 7 months ago #4069
by xavier
Replied by xavier on topic Parametrizing new molecule with backward.py
Could it be that your lipid is just jumping across the PBC on the z direction?
You could try to increase the box dimensions so the lipid does to jump …
You could try to increase the box dimensions so the lipid does to jump …
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