[gmx-users] Simulating infinite polymer crystal structure
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 29 19:58:02 CET 2005
Malin Bergenstråhle wrote:
> 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.
>
it could be a problem in the topology, that only shows occasionally. Do
you happen to have 1-4 interactions between groups that only have
Coulomb attraction? An example such might be a protonated acid, where
the H on one O might be fatally attracted to the other O.
> 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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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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