[gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?

[Du, Yu]

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 
[ 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