[gmx-users] Hydrogens of ATB ligand show obvious vibration under all-bonds contraints?
Billy Williams-Noonan
billy.williams-noonan at monash.edu
Sun Oct 20 15:31:16 CEST 2019
Apologies for the typo, the methylene group should also be united atom
Good luck!
On Sun., 20 Oct. 2019, 11:42 pm Du, Yu, <duyu at sioc.ac.cn> wrote:
> Hi Billy,
>
> Thanks for your remind. I indeed used the all-atom topology of melatonin
> from ATB
> (offers both all- and united- atom versions for small molecules). I will
> change to
> the united-atom version.
>
> Sincerely,
> Yu
>
>
> > -----Original Messages-----
> > From: "Billy Williams-Noonan" <billy.williams-noonan at monash.edu>
> > Sent Time: 2019-10-20 11:45:40 (Sunday)
> > To: gmx-users at gromacs.org
> > Cc:
> > Subject: Re: [gmx-users] Hydrogens of ATB ligand show obvious vibration
> under all-bonds contraints?
> >
> > Hi Yu,
> >
> > I don't think the methyl group should have hydrogens explicitly specified
> > with the Gromos force field. The methyl group should be one united atom
> >
> > The methylene group is okay though.
> >
> > Cheers,
> > Billy
> >
> > On Sat., 19 Oct. 2019, 1:06 pm Du, Yu, <duyu at sioc.ac.cn> wrote:
> >
> > > 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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> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
>
> --
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