[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 05:45:55 CEST 2019
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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