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

Du, Yu duyu at sioc.ac.cn
Sat Oct 19 04:06:07 CEST 2019


Dear GMX-Users,

The vibration of the hydrogens of methyl and methylene groups was the result of 
Trajectory Smoothing in VMD, not the problem of GROMACS's all-bond constraints.

Sorry for this distracting question.

Yu


> -----Original Messages-----
> From: "Du, Yu" <duyu at sioc.ac.cn>
> Sent Time: 2019-10-18 08:20:10 (Friday)
> To: gmx-users at gromacs.org
> Cc: 
> Subject: Re: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?
> 
> Hi Justin, 
> 
> Thanks for your reply.
> I will use the united-atom topology of the ligand.
> 
> Yu
> 
> 
> > -----Original Messages-----
> > From: "Justin Lemkul" <jalemkul at vt.edu>
> > Sent Time: 2019-10-17 23:17:47 (Thursday)
> > To: gmx-users at gromacs.org
> > Cc: 
> > Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?
> > 
> > 
> > 
> > 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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