[gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?
Justin Lemkul
jalemkul at vt.edu
Thu Oct 17 17:17:59 CEST 2019
On 10/17/19 11:02 AM, Du, Yu wrote:
> Dear GMX-Users,
>
> I'm using GMX2018.3 simulating Melatonin (ATB Link: https://atb.uq.edu.au/molecule.py?molid=355098).
>
>
> I found that the hydrogens of two methyl groups (CH3, i.e. CH11, CH12, CH13, CH14, CH15 and CH16) showed
> obvious vibration under the following mdp configuration:
>
>
> integrator = md
> dt = 0.002
> cutoff-scheme = group
> constraints = all-bonds
> constraint_algorithm = lincs
> continuation = yes
>
>
> I used the gromos54a7_atb.ff.
>
>
>
>
> P.S. The partial topology of Melatonin from ATB
You're using the wrong topology. GROMOS parameter sets are united-atom,
but you've chosen the all-atom topology (no idea why this exists,
honestly). Your CH3 and CH2 groups should have no explicit H atoms.
-Justin
> [ moleculetype ]
> ; Name nrexcl
> ESV6 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 HC 1 ESV6 H16 1 0.067 1.0080
> 2 CPos 1 ESV6 C13 2 0.010 12.0110
> 3 HC 1 ESV6 H14 3 0.067 1.0080
> 4 HC 1 ESV6 H15 4 0.067 1.0080
> 5 OE 1 ESV6 O1 5 -0.368 15.9994
> 6 CAro 1 ESV6 C9 6 0.398 12.0110
> 7 CAro 1 ESV6 C7 7 -0.385 12.0110
> 8 HC 1 ESV6 H7 8 0.163 1.0080
> 9 CAro 1 ESV6 C2 9 0.085 12.0110
> 10 CAro 1 ESV6 C1 10 -0.057 12.0110
> 11 CAro 1 ESV6 C5 11 -0.144 12.0110
> 12 HC 1 ESV6 H3 12 0.186 1.0080
> 13 NOpt 1 ESV6 N1 13 -0.354 14.0067
> 14 HS14 1 ESV6 H6 14 0.373 1.0080
> 15 CAro 1 ESV6 C4 15 0.070 12.0110
> 16 CAro 1 ESV6 C8 16 -0.145 12.0110
> 17 HC 1 ESV6 H8 17 0.156 1.0080
> 18 CAro 1 ESV6 C10 18 -0.360 12.0110
> 19 HC 1 ESV6 H9 19 0.169 1.0080
> 20 C 1 ESV6 C3 20 -0.159 12.0110
> 21 HC 1 ESV6 H1 21 0.070 1.0080
> 22 HC 1 ESV6 H2 22 0.070 1.0080
> 23 CPos 1 ESV6 C6 23 0.231 12.0110
> 24 HC 1 ESV6 H4 24 0.014 1.0080
> 25 HC 1 ESV6 H5 25 0.014 1.0080
> 26 N 1 ESV6 N2 26 -0.525 14.0067
> 27 HS14 1 ESV6 H10 27 0.307 1.0080
> 28 CPos 1 ESV6 C11 28 0.684 12.0110
> 29 OEOpt 1 ESV6 O2 29 -0.616 15.9994
> 30 C 1 ESV6 C12 30 -0.586 12.0110
> 31 HC 1 ESV6 H11 31 0.166 1.0080
> 32 HC 1 ESV6 H12 32 0.166 1.0080
> 33 HC 1 ESV6 H13 33 0.166 1.0080
> ; total charge of the molecule: 0.000
> [ bonds ]
> ; ai aj funct c0 c1
> 1 2 2 0.1090 1.2300e+07
> 2 3 2 0.1090 1.2300e+07
> 2 4 2 0.1090 1.2300e+07
> 2 5 2 0.1430 8.1800e+06
> 5 6 2 0.1380 4.4633e+06
> 6 7 2 0.1390 8.6600e+06
> 6 18 2 0.1420 3.2236e+06
> 7 8 2 0.1090 1.2300e+07
> 7 9 2 0.1410 6.5389e+06
> 9 10 2 0.1435 6.1000e+06
> 9 15 2 0.1430 8.1800e+06
> 10 11 2 0.1380 1.1000e+07
> 10 20 2 0.1500 8.3700e+06
> 11 12 2 0.1090 1.2300e+07
> 11 13 2 0.1380 1.1000e+07
> 13 14 2 0.1010 6.3719e+06
> 13 15 2 0.1380 1.1000e+07
> 15 16 2 0.1400 8.5400e+06
> 16 17 2 0.1090 1.2300e+07
> 16 18 2 0.1390 8.6600e+06
> 18 19 2 0.1090 1.2300e+07
> 20 21 2 0.1090 1.2300e+07
> 20 22 2 0.1090 1.2300e+07
> 20 23 2 0.1540 4.0057e+06
> 23 24 2 0.1090 1.2300e+07
> 23 25 2 0.1090 1.2300e+07
> 23 26 2 0.1460 4.6913e+06
> 26 27 2 0.1010 6.3719e+06
> 26 28 2 0.1360 1.0200e+07
> 28 29 2 0.1230 1.6600e+07
> 28 30 2 0.1520 5.4300e+06
> 30 31 2 0.1090 1.2300e+07
> 30 32 2 0.1090 1.2300e+07
> 30 33 2 0.1090 1.2300e+07
>
>
>
>
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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