[gmx-users] Simulating infinite polymer crystal structure
Malin Bergenstråhle
malbe at kth.se
Thu Dec 29 19:07:36 CET 2005
Yes, I have minimized the system initially and I use quite a small timestep of 1 fs. I have also tried to decrease the timestep even more but it does not help.
I use normal MD with Berendsen thermostat at 298 K.
What is strange is that it is sometimes possible to simulate a couple of ns without problem, but then suddenly these rotations start and then it is almost impossible to continue with that structure.
Malin
Hi,
I don't have any experience with polymers, but these sorts of errors
often happen when forces get too large for some reason. Have you
minimized your system well initially? What timestep are you using? Are
you just running simple MD, and with what thermostat? Sometimes using
a smaller timestep can help.
David
On 12/29/05, Malin Bergenstråhle <malbe at kth.se> wrote:
>> 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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