[gmx-users] Simulating infinite polymer crystal structure
Malin Bergenstråhle
malbe at kth.se
Thu Dec 29 15:44:53 CET 2005
Hi all,
I am trying to simulate a system consisting of 16 infinite polymer
chains in a crystal structure.
I have a lot of troubles with simulations crashing due to Lincs
complaining about rotating bonds (see dump from a typical logfile below).
My system is organized with the 16 chains in 4 layers with 4 chains
each. The two central layers are position restrained to act bulk and the
outer 8 chains are allowed to move.
I have not been able to figure out what causes the crashes but it seems
as if two atoms get very close to eachother and then suddenly one of
them start rotating. I wonder if anybody has experience from simulating
infinite crystal polymer structures before? The polymer I am using is
cellulose with 2 cellobiose units per chain.
One specific thing that I wonder if it could cause such problems is that
my system is not relaxed, the 2 central layers are fixed in the
experimental crystal structure. Although, when I try simulating one
chain it works fine and also sometimes with the whole system it works,
it is just very very unreliable and when it starts crashing it is
difficult to get it stable again.
Any comments would be nice.
Thanks,
Malin
Step 47430, time 47.43 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.028302 (between atoms 5 and 6) rms 0.000658
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4 5 46.2 0.1435 0.1424 0.1435
5 6 67.2 0.1000 0.1028 0.1000
81 82 47.6 0.1000 0.1012 0.1000
Step 47431, time 47.431 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.076858 (between atoms 5 and 6) rms 0.001591
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4 5 35.6 0.1424 0.1424 0.1435
5 6 94.5 0.1028 0.1077 0.1000
81 82 45.8 0.1012 0.1001 0.1000
Step 47432, time 47.432 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 12.802402 (between atoms 4 and 5) rms 0.411134
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 94.6 0.1435 0.2582 0.1435
1 7 36.8 0.1520 0.1925 0.1520
56 1 48.5 0.1435 0.2066 0.1435
2 3 100.5 0.1435 0.6530 0.1435
3 4 102.7 0.1519 0.5980 0.1520
3 13 98.9 0.1520 0.7495 0.1520
4 5 94.6 0.1424 1.9806 0.1435
5 6 96.0 0.1077 0.9881 0.1000
7 10 52.7 0.1520 0.2386 0.1520
10 11 55.6 0.1435 0.2351 0.1435
10 13 95.9 0.1520 1.0668 0.1520
13 14 100.1 0.1435 0.6664 0.1435
14 15 94.4 0.1435 1.2567 0.1435
15 16 105.2 0.1435 0.4742 0.1435
15 21 100.7 0.1520 0.3847 0.1520
16 17 73.0 0.1435 0.2353 0.1435
17 18 31.8 0.1520 0.1793 0.1520
21 22 73.8 0.1435 0.2583 0.1435
21 24 67.5 0.1520 0.2454 0.1520
22 23 54.5 0.1000 0.1558 0.1000
24 25 31.7 0.1435 0.1708 0.1435
81 82 42.0 0.1001 0.0990 0.1000
Constraint error in algorithm Lincs at step 47432
Wrote pdb files with previous and current coordinates
Step 47433, time 47.433 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 134.873215 (between atoms 21 and 22) rms 6.610656
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 113.0 0.2582 0.7208 0.1435
1 7 103.7 0.1925 4.1936 0.1520
56 1 120.7 0.2066 0.6874 0.1435
2 3 150.9 0.6530 0.9020 0.1435
3 4 102.2 0.5980 3.6322 0.1520
3 13 56.7 0.7495 1.9560 0.1520
4 5 88.7 1.9806 5.8247 0.1435
5 6 95.7 0.9881 0.5766 0.1000
7 8 81.8 0.1581 3.7805 0.1435
7 10 104.3 0.2386 3.2932 0.1520
8 9 129.8 0.1026 0.4876 0.1000
10 11 106.4 0.2351 1.2224 0.1435
10 13 85.0 1.0668 0.9720 0.1520
11 12 93.3 0.1030 0.0923 0.1000
13 14 87.2 0.6664 4.4932 0.1435
14 15 71.9 1.2567 4.8085 0.1435
15 16 57.0 0.4742 3.4035 0.1435
15 21 91.6 0.3847 17.6591 0.1520
16 17 105.4 0.2353 18.8067 0.1435
17 18 90.5 0.1793 15.4891 0.1520
17 27 163.1 0.1688 4.7973 0.1520
18 19 128.8 0.1473 3.0623 0.1435
19 20 131.1 0.1004 1.4866 0.1000
21 22 59.0 0.2583 19.4978 0.1435
21 24 75.0 0.2454 18.2038 0.1520
22 23 69.8 0.1558 3.1969 0.1000
24 27 95.0 0.1705 18.0591 0.1520
25 26 95.1 0.1043 2.0528 0.1000
27 28 92.3 0.1504 11.2440 0.1435
28 29 56.5 0.1455 3.3040 0.1435
29 30 66.7 0.1439 1.4205 0.1435
29 35 115.3 0.1525 1.5023 0.1520
30 31 115.1 0.1435 0.0240 0.1435
31 41 39.6 0.1520 0.1845 0.1520
35 36 123.8 0.1436 0.2553 0.1435
35 38 125.4 0.1521 0.2678 0.1520
36 37 58.7 0.1000 0.1677 0.1000
38 39 44.9 0.1435 0.2033 0.1435
38 41 45.8 0.1520 0.2244 0.1520
44 45 49.6 0.1440 0.2112 0.1435
45 46 52.2 0.1525 0.2301 0.1520
45 55 92.2 0.1542 0.3725 0.1520
49 52 53.2 0.1524 0.2378 0.1520
52 53 54.4 0.1438 0.2240 0.1435
52 55 92.5 0.1538 0.3668 0.1520
55 56 85.8 0.1497 0.3253 0.1435
81 82 33.7 0.0990 0.0994 0.1000
Constraint error in algorithm Lincs at step 47433
Wrote pdb files with previous and current coordinates
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