# Triple bond oscillation **URL:** \ **Category:** User discussions\ **Created:** [August 13, 2022, 7:13am UTC](https://gromacs.bioexcel.eu/t/triple-bond-oscillation/4601 "2022-08-13T07:13:50Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![galmasrati](https://avatars.discourse-cdn.com/v4/letter/g/b9e5f3/32.png) [@galmasrati](https://gromacs.bioexcel.eu/u/galmasrati)\ **Post date:** [August 13, 2022, 7:13am UTC](https://gromacs.bioexcel.eu/t/triple-bond-oscillation/4601/1 "2022-08-13T07:13:50Z")
GROMACS version: 2021.2 GROMACS modification: No Hi All, I’m trying to simulate a complex of a protein bound to a small molecule from the Protein Data Bank. I parameterized the small molecule using acpype (see the head of the itp file below). During the first steps of equilibration grompp gives the following note: The bond in molecule-type MOL between atoms 60 C32 and 61 C33 has an estimated oscillational period of 1.9e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. I do not want to set constraints to “all-bonds”. I also know that setting dt to 1 fs will make this note go away, but I was wondering if there are other solutions. I tried to use different force-fields and parameters (Charmm and OPLS) but it doesn’t make a difference. Any thoughts would be much appreciated! Cheers. **The itp file:** [moleculetype] ;name nrexcl MOL 3 [atoms] ; nr type resi res atom cgnr charge mass ; qtot bond\_type 1 ca 1 MOL C22 1 -0.150000 12.01000 ; qtot -0.150 2 ha 1 MOL HC22 1 0.172000 1.00800 ; qtot 0.022 3 ca 1 MOL C21 2 -0.075000 12.01000 ; qtot -0.053 4 ha 1 MOL HC21 2 0.158000 1.00800 ; qtot 0.105 5 ca 1 MOL C23 3 0.174900 12.01000 ; qtot 0.280 6 ca 1 MOL C20 4 0.014000 12.01000 ; qtot 0.294 7 ca 1 MOL C24 5 -0.033000 12.01000 ; qtot 0.261 8 ca 1 MOL C19 6 -0.022000 12.01000 ; qtot 0.239 9 ca 1 MOL C17 7 0.127100 12.01000 ; qtot 0.366 10 c3 1 MOL C14 8 -0.107400 12.01000 ; qtot 0.259 11 hc 1 MOL H141 8 0.103200 1.00800 ; qtot 0.362 12 hc 1 MOL H142 8 0.103200 1.00800 ; qtot 0.465 13 c3 1 MOL C13 9 0.171300 12.01000 ; qtot 0.636 14 h1 1 MOL H131 9 0.103200 1.00800 ; qtot 0.740 15 h1 1 MOL H132 9 0.103200 1.00800 ; qtot 0.843 16 ca 1 MOL C18 10 -0.174000 12.01000 ; qtot 0.669 17 ha 1 MOL HC18 10 0.157000 1.00800 ; qtot 0.826 18 ca 1 MOL C01 11 -0.381900 12.01000 ; qtot 0.444 19 ca 1 MOL C02 12 0.430600 12.01000 ; qtot 0.874 20 ca 1 MOL C03 13 0.853300 12.01000 ; qtot 1.728 21 ca 1 MOL C04 14 0.710200 12.01000 ; qtot 2.438 22 ca 1 MOL C05 15 0.441200 12.01000 ; qtot 2.879 23 h4 1 MOL HC05 15 0.042100 1.00800 ; qtot 2.921 24 cp 1 MOL C06 16 0.515800 12.01000 ; qtot 3.437 25 ca 1 MOL C07 17 -0.032700 12.01000 ; qtot 3.404 26 cp 1 MOL C08 18 -0.150500 12.01000 ; qtot 3.254 27 c3 1 MOL C09 19 0.124400 12.01000 ; qtot 3.378 28 h1 1 MOL H091 19 0.100700 1.00800 ; qtot 3.479 29 h1 1 MOL H092 19 0.100700 1.00800 ; qtot 3.580 30 c3 1 MOL C10 20 0.171300 12.01000 ; qtot 3.751 31 h1 1 MOL H101 20 0.103200 1.00800 ; qtot 3.854 32 h1 1 MOL H102 20 0.103200 1.00800 ; qtot 3.957 33 c3 1 MOL C11 21 0.109000 12.01000 ; qtot 4.066 34 hx 1 MOL HC11 21 0.135700 1.00800 ; qtot 4.202 35 c3 1 MOL C12 22 0.109000 12.01000 ; qtot 4.311 36 hx 1 MOL HC12 22 0.135700 1.00800 ; qtot 4.447 37 c3 1 MOL C15 23 -0.107400 12.01000 ; qtot 4.339 38 hc 1 MOL H151 23 0.103200 1.00800 ; qtot 4.442 39 hc 1 MOL H152 23 0.103200 1.00800 ; qtot 4.546 40 ca 1 MOL C16 24 -0.093000 12.01000 ; qtot 4.453 41 ha 1 MOL HC16 24 0.156000 1.00800 ; qtot 4.609 42 c3 1 MOL C25 25 0.121200 12.01000 ; qtot 4.730 43 c3 1 MOL C26 26 -0.126400 12.01000 ; qtot 4.603 44 hc 1 MOL H261 26 0.100700 1.00800 ; qtot 4.704 45 hc 1 MOL H262 26 0.100700 1.00800 ; qtot 4.805 46 c3 1 MOL C27 27 0.176600 12.01000 ; qtot 4.981 47 h1 1 MOL HC27 27 0.115700 1.00800 ; qtot 5.097 48 c3 1 MOL C28 28 0.074800 12.01000 ; qtot 5.172 49 hx 1 MOL H281 28 0.126200 1.00800 ; qtot 5.298 50 hx 1 MOL H282 28 0.126200 1.00800 ; qtot 5.424 51 c3 1 MOL C29 29 0.115800 12.01000 ; qtot 5.540 52 hx 1 MOL H291 29 0.108200 1.00800 ; qtot 5.648 53 hx 1 MOL H292 29 0.108200 1.00800 ; qtot 5.757 54 c3 1 MOL C30 30 -0.100400 12.01000 ; qtot 5.656 55 hc 1 MOL H301 30 0.095700 1.00800 ; qtot 5.752 56 hc 1 MOL H302 30 0.095700 1.00800 ; qtot 5.848 57 c3 1 MOL C31 31 -0.096400 12.01000 ; qtot 5.751 58 hc 1 MOL H311 31 0.096700 1.00800 ; qtot 5.848 59 hc 1 MOL H312 31 0.096700 1.00800 ; qtot 5.945 60 cg 1 MOL C32 32 -0.102000 12.01000 ; qtot 5.843 61 c1 1 MOL C33 33 -0.163500 12.01000 ; qtot 5.679 62 ha 1 MOL HC33 33 0.163500 1.00800 ; qtot 5.843 63 f 1 MOL F01 34 -0.104900 19.00000 ; qtot 5.738 64 f 1 MOL F02 35 -0.205300 19.00000 ; qtot 5.532 65 f 1 MOL F23 36 -0.117900 19.00000 ; qtot 5.414 66 nb 1 MOL N01 37 -0.738000 14.01000 ; qtot 4.676 67 nb 1 MOL N02 38 -0.753000 14.01000 ; qtot 3.923 68 nb 1 MOL N03 39 -0.597000 14.01000 ; qtot 3.326 69 nh 1 MOL N04 40 -0.763300 14.01000 ; qtot 2.563 70 ny 1 MOL N05 41 -0.785000 14.01000 ; qtot 1.778 71 hn 1 MOL H051 41 0.463800 1.00800 ; qtot 2.242 72 hn 1 MOL H052 41 0.463800 1.00800 ; qtot 2.706 73 nx 1 MOL N06 42 -0.679400 14.01000 ; qtot 2.026 74 hn 1 MOL HN06 42 0.467800 1.00800 ; qtot 2.494 75 os 1 MOL O01 43 -0.444100 16.00000 ; qtot 2.050 76 oh 1 MOL O02 44 -0.487100 16.00000 ; qtot 1.563 77 ho 1 MOL HO02 44 0.437000 1.00800 ; qtot 2.000 [bonds] ; ai aj funct r k 1 2 1 1.0860e-01 3.3112e+05 ; C22 - HC22 1 3 1 1.3980e-01 3.1681e+05 ; C22 - C21 1 5 1 1.3980e-01 3.1681e+05 ; C22 - C23 3 4 1 1.0860e-01 3.3112e+05 ; C21 - HC21 3 8 1 1.3980e-01 3.1681e+05 ; C21 - C19 5 7 1 1.3980e-01 3.1681e+05 ; C23 - C24 5 65 1 1.3490e-01 2.9589e+05 ; C23 - F23 6 7 1 1.3980e-01 3.1681e+05 ; C20 - C24 6 8 1 1.3980e-01 3.1681e+05 ; C20 - C19 6 26 1 1.4060e-01 3.0828e+05 ; C20 - C08 7 60 1 1.4330e-01 2.7957e+05 ; C24 - C32 8 16 1 1.3980e-01 3.1681e+05 ; C19 - C18 9 16 1 1.3980e-01 3.1681e+05 ; C17 - C18 9 40 1 1.3980e-01 3.1681e+05 ; C17 - C16 9 76 1 1.3640e-01 3.0593e+05 ; C17 - O02 10 11 1 1.0970e-01 3.1455e+05 ; C14 - H141 10 12 1 1.0970e-01 3.1455e+05 ; C14 - H142 10 35 1 1.5380e-01 1.9456e+05 ; C14 - C12 10 37 1 1.5380e-01 1.9456e+05 ; C14 - C15 13 14 1 1.0970e-01 3.1455e+05 ; C13 - H131 13 15 1 1.0970e-01 3.1455e+05 ; C13 - H132 13 35 1 1.5380e-01 1.9456e+05 ; C13 - C12 13 69 1 1.4640e-01 2.1907e+05 ; C13 - N04 16 17 1 1.0860e-01 3.3112e+05 ; C18 - HC18 18 19 1 1.3980e-01 3.1681e+05 ; C01 - C02 18 21 1 1.3980e-01 3.1681e+05 ; C01 - C04 18 22 1 1.3980e-01 3.1681e+05 ; C01 - C05 19 25 1 1.3980e-01 3.1681e+05 ; C02 - C07 19 66 1 1.3390e-01 3.4660e+05 ; C02 - N01 20 66 1 1.3390e-01 3.4660e+05 ; C03 - N01 20 67 1 1.3390e-01 3.4660e+05 ; C03 - N02 20 75 1 1.3700e-01 2.9916e+05 ; C03 - O01 21 67 1 1.3390e-01 3.4660e+05 ; C04 - N02 21 69 1 1.3860e-01 2.9045e+05 ; C04 - N04 22 23 1 1.0890e-01 3.2644e+05 ; C05 - HC05 22 68 1 1.3390e-01 3.4660e+05 ; C05 - N03 24 25 1 1.4060e-01 3.0828e+05 ; C06 - C07 24 26 1 1.4850e-01 2.3230e+05 ; C06 - C08 24 68 1 1.3390e-01 3.4702e+05 ; C06 - N03 25 63 1 1.3490e-01 2.9589e+05 ; C07 - F01 26 40 1 1.4060e-01 3.0828e+05 ; C08 - C16 27 28 1 1.0970e-01 3.1455e+05 ; C09 - H091 27 29 1 1.0970e-01 3.1455e+05 ; C09 - H092 27 42 1 1.5380e-01 1.9456e+05 ; C09 - C25 27 75 1 1.4320e-01 2.3832e+05 ; C09 - O01 30 31 1 1.0970e-01 3.1455e+05 ; C10 - H101 30 32 1 1.0970e-01 3.1455e+05 ; C10 - H102 30 33 1 1.5380e-01 1.9456e+05 ; C10 - C11 30 69 1 1.4640e-01 2.1907e+05 ; C10 - N04 33 34 1 1.0910e-01 3.2342e+05 ; C11 - HC11 33 37 1 1.5380e-01 1.9456e+05 ; C11 - C15 33 70 1 1.5110e-01 1.8627e+05 ; C11 - N05 35 36 1 1.0910e-01 3.2342e+05 ; C12 - HC12 35 70 1 1.5110e-01 1.8627e+05 ; C12 - N05 37 38 1 1.0970e-01 3.1455e+05 ; C15 - H151 37 39 1 1.0970e-01 3.1455e+05 ; C15 - H152 40 41 1 1.0860e-01 3.3112e+05 ; C16 - HC16 42 43 1 1.5380e-01 1.9456e+05 ; C25 - C26 42 57 1 1.5380e-01 1.9456e+05 ; C25 - C31 42 73 1 1.5110e-01 1.8627e+05 ; C25 - N06 43 44 1 1.0970e-01 3.1455e+05 ; C26 - H261 43 45 1 1.0970e-01 3.1455e+05 ; C26 - H262 43 46 1 1.5380e-01 1.9456e+05 ; C26 - C27 46 47 1 1.0970e-01 3.1455e+05 ; C27 - HC27 46 48 1 1.5380e-01 1.9456e+05 ; C27 - C28 46 64 1 1.3500e-01 2.9506e+05 ; C27 - F02 48 49 1 1.0910e-01 3.2342e+05 ; C28 - H281 48 50 1 1.0910e-01 3.2342e+05 ; C28 - H282 48 73 1 1.5110e-01 1.8627e+05 ; C28 - N06 51 52 1 1.0910e-01 3.2342e+05 ; C29 - H291 51 53 1 1.0910e-01 3.2342e+05 ; C29 - H292 51 54 1 1.5380e-01 1.9456e+05 ; C29 - C30 51 73 1 1.5110e-01 1.8627e+05 ; C29 - N06 54 55 1 1.0970e-01 3.1455e+05 ; C30 - H301 54 56 1 1.0970e-01 3.1455e+05 ; C30 - H302 54 57 1 1.5380e-01 1.9456e+05 ; C30 - C31 57 58 1 1.0970e-01 3.1455e+05 ; C31 - H311 57 59 1 1.0970e-01 3.1455e+05 ; C31 - H312 60 61 1 1.2160e-01 6.5003e+05 ; C32 - C33 61 62 1 1.0670e-01 3.6292e+05 ; C33 - HC33 70 71 1 1.0300e-01 4.0409e+05 ; N05 - H051 70 72 1 1.0300e-01 4.0409e+05 ; N05 - H052 73 74 1 1.0300e-01 4.0409e+05 ; N06 - HN06 76 77 1 9.7300e-02 4.7154e+05 ; O02 - HO02 [pairs] ; ai aj funct 1 6 1 ; C22 - C20 1 16 1 ; C22 - C18 1 60 1 ; C22 - C32 2 4 1 ; HC22 - HC21 2 7 1 ; HC22 - C24 2 8 1 ; HC22 - C19 2 65 1 ; HC22 - F23 3 7 1 ; C21 - C24 3 9 1 ; C21 - C17 3 17 1 ; C21 - HC18 3 26 1 ; C21 - C08 3 65 1 ; C21 - F23 5 4 1 ; C23 - HC21 5 8 1 ; C23 - C19 5 26 1 ; C23 - C08 5 61 1 ; C23 - C33 6 4 1 ; C20 - HC21 6 9 1 ; C20 - C17 6 17 1 ; C20 - HC18 6 25 1 ; C20 - C07 6 41 1 ; C20 - HC16 6 61 1 ; C20 - C33 6 65 1 ; C20 - F23 6 68 1 ; C20 - N03 7 16 1 ; C24 - C18 7 24 1 ; C24 - C06 7 40 1 ; C24 - C16 7 62 1 ; C24 - HC33 8 24 1 ; C19 - C06 8 40 1 ; C19 - C16 8 60 1 ; C19 - C32 8 76 1 ; C19 - O02 9 24 1 ; C17 - C06 10 14 1 ; C14 - H131 10 15 1 ; C14 - H132 10 30 1 ; C14 - C10 10 34 1 ; C14 - HC11 10 69 1 ; C14 - N04 10 71 1 ; C14 - H051 10 72 1 ; C14 - H052 11 36 1 ; H141 - HC12 11 38 1 ; H141 - H151 11 39 1 ; H141 - H152 12 36 1 ; H142 - HC12 12 38 1 ; H142 - H151 12 39 1 ; H142 - H152 13 11 1 ; C13 - H141 13 12 1 ; C13 - H142 13 18 1 ; C13 - C01 13 31 1 ; C13 - H101 13 32 1 ; C13 - H102 13 33 1 ; C13 - C11 13 37 1 ; C13 - C15 13 67 1 ; C13 - N02 13 71 1 ; C13 - H051 13 72 1 ; C13 - H052 14 36 1 ; H131 - HC12 15 36 1 ; H132 - HC12 16 4 1 ; C18 - HC21 16 26 1 ; C18 - C08 16 41 1 ; C18 - HC16 16 77 1 ; C18 - HO02 18 20 1 ; C01 - C03 18 24 1 ; C01 - C06 18 30 1 ; C01 - C10 18 63 1 ; C01 - F01 19 23 1 ; C02 - HC05 19 26 1 ; C02 - C08 19 67 1 ; C02 - N02 19 68 1 ; C02 - N03 19 69 1 ; C02 - N04 19 75 1 ; C02 - O01 20 25 1 ; C03 - C07 20 28 1 ; C03 - H091 20 29 1 ; C03 - H092 20 42 1 ; C03 - C25 20 69 1 ; C03 - N04 21 14 1 ; C04 - H131 21 15 1 ; C04 - H132 21 23 1 ; C04 - HC05 21 25 1 ; C04 - C07 21 31 1 ; C04 - H101 21 32 1 ; C04 - H102 21 33 1 ; C04 - C11 21 35 1 ; C04 - C12 21 66 1 ; C04 - N01 21 68 1 ; C04 - N03 21 75 1 ; C04 - O01 22 25 1 ; C05 - C07 22 26 1 ; C05 - C08 22 66 1 ; C05 - N01 22 67 1 ; C05 - N02 22 69 1 ; C05 - N04 24 23 1 ; C06 - HC05 24 41 1 ; C06 - HC16 24 66 1 ; C06 - N01 25 40 1 ; C07 - C16 26 60 1 ; C08 - C32 26 63 1 ; C08 - F01 26 76 1 ; C08 - O02 27 44 1 ; C09 - H261 27 45 1 ; C09 - H262 27 46 1 ; C09 - C27 27 48 1 ; C09 - C28 27 51 1 ; C09 - C29 27 54 1 ; C09 - C30 27 58 1 ; C09 - H311 27 59 1 ; C09 - H312 27 66 1 ; C09 - N01 27 67 1 ; C09 - N02 27 74 1 ; C09 - HN06 30 14 1 ; C10 - H131 30 15 1 ; C10 - H132 30 35 1 ; C10 - C12 30 38 1 ; C10 - H151 30 39 1 ; C10 - H152 30 67 1 ; C10 - N02 30 71 1 ; C10 - H051 30 72 1 ; C10 - H052 31 34 1 ; H101 - HC11 32 34 1 ; H102 - HC11 33 11 1 ; C11 - H141 33 12 1 ; C11 - H142 33 36 1 ; C11 - HC12 34 38 1 ; HC11 - H151 34 39 1 ; HC11 - H152 34 71 1 ; HC11 - H051 34 72 1 ; HC11 - H052 35 34 1 ; C12 - HC11 35 38 1 ; C12 - H151 35 39 1 ; C12 - H152 36 71 1 ; HC12 - H051 36 72 1 ; HC12 - H052 37 31 1 ; C15 - H101 37 32 1 ; C15 - H102 37 36 1 ; C15 - HC12 37 69 1 ; C15 - N04 37 71 1 ; C15 - H051 37 72 1 ; C15 - H052 40 17 1 ; C16 - HC18 40 68 1 ; C16 - N03 40 77 1 ; C16 - HO02 42 47 1 ; C25 - HC27 42 49 1 ; C25 - H281 42 50 1 ; C25 - H282 42 52 1 ; C25 - H291 42 53 1 ; C25 - H292 42 55 1 ; C25 - H301 42 56 1 ; C25 - H302 42 64 1 ; C25 - F02 43 28 1 ; C26 - H091 43 29 1 ; C26 - H092 43 49 1 ; C26 - H281 43 50 1 ; C26 - H282 43 51 1 ; C26 - C29 43 54 1 ; C26 - C30 43 58 1 ; C26 - H311 43 59 1 ; C26 - H312 43 74 1 ; C26 - HN06 43 75 1 ; C26 - O01 44 47 1 ; H261 - HC27 45 47 1 ; H262 - HC27 46 51 1 ; C27 - C29 46 57 1 ; C27 - C31 46 74 1 ; C27 - HN06 47 49 1 ; HC27 - H281 47 50 1 ; HC27 - H282 48 44 1 ; C28 - H261 48 45 1 ; C28 - H262 48 52 1 ; C28 - H291 48 53 1 ; C28 - H292 48 54 1 ; C28 - C30 48 57 1 ; C28 - C31 49 74 1 ; H281 - HN06 50 74 1 ; H282 - HN06 51 49 1 ; C29 - H281 51 50 1 ; C29 - H282 51 58 1 ; C29 - H311 51 59 1 ; C29 - H312 52 55 1 ; H291 - H301 52 56 1 ; H291 - H302 52 74 1 ; H291 - HN06 53 55 1 ; H292 - H301 53 56 1 ; H292 - H302 53 74 1 ; H292 - HN06 54 74 1 ; C30 - HN06 55 58 1 ; H301 - H311 55 59 1 ; H301 - H312 56 58 1 ; H302 - H311 56 59 1 ; H302 - H312 57 28 1 ; C31 - H091 57 29 1 ; C31 - H092 57 44 1 ; C31 - H261 57 45 1 ; C31 - H262 57 52 1 ; C31 - H291 57 53 1 ; C31 - H292 57 74 1 ; C31 - HN06 57 75 1 ; C31 - O01 60 65 1 ; C32 - F23 63 66 1 ; F01 - N01 63 68 1 ; F01 - N03 64 44 1 ; F02 - H261 64 45 1 ; F02 - H262 64 49 1 ; F02 - H281 64 50 1 ; F02 - H282 64 73 1 ; F02 - N06 69 34 1 ; N04 - HC11 69 36 1 ; N04 - HC12 69 70 1 ; N04 - N05 70 11 1 ; N05 - H141 70 12 1 ; N05 - H142 70 14 1 ; N05 - H131 70 15 1 ; N05 - H132 70 31 1 ; N05 - H101 70 32 1 ; N05 - H102 70 38 1 ; N05 - H151 70 39 1 ; N05 - H152 73 28 1 ; N06 - H091 73 29 1 ; N06 - H092 73 44 1 ; N06 - H261 73 45 1 ; N06 - H262 73 47 1 ; N06 - HC27 73 55 1 ; N06 - H301 73 56 1 ; N06 - H302 73 58 1 ; N06 - H311 73 59 1 ; N06 - H312 73 75 1 ; N06 - O01 76 17 1 ; O02 - HC18 76 41 1 ; O02 - HC16 ---
**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\ **Post date:** [August 14, 2022, 3:29pm UTC](https://gromacs.bioexcel.eu/t/triple-bond-oscillation/4601/2 "2022-08-14T15:29:00Z")
> [@galmasrati](#): > > 1.9e-02 ps, which is less than 10 times > the time step of 2.0e-03 ps. > Maybe you forgot to change the constraints mdp option. > > I do not want to set constraints to “all-bonds”. I also know that setting dt to 1 fs will make this note go away, but I was wondering if there are other solutions. I simulate with dt = 0.0015, you don’t need to use dt = 0.001 It is important for you to have dt \<= 0.0019. (I use the time step 0.0015 because it is easier to process such a trajectory in the analyzes than, for example, 0.0019). The computational cost will be greater, but the simulation will be more accurate and correct.