Hi Justin, Thanks for your reply. I will use the united-atom topology of the ligand.
Yu > -----Original Messages----- > From: "Justin Lemkul" <jalem...@vt.edu> > Sent Time: 2019-10-17 23:17:47 (Thursday) > To: gmx-us...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.