Hi,
Not sure if it was also you, but I recall replying not so long ago to a QM/MM question that all QM atoms must by inside the same topology (itp or top) for gromacs 4 and beyond. Splitting the QM atoms over multiple topologies leads to erroneous behaviour. I don't know for sure if this is also the reason for the crahs, but considering that the some atoms are missing some forces it could be. Best, gerrit Today's Topics: 1. Re: 5. LINCS warning of QMMM simulation (andrian) (andrian) Hi Gerrit and all users, do you have an idea about this problem ? now, i attached all my simulation files... hope someone can help.. thanks in advance cheers On 27/04/16 01:48, Groenhof, Gerrit wrote: > Hi, > > Are you able to run a stable MM simulation with that system? > > Can you rule out that the system is not strained somewhere? > > Where do the starting coordinates come from? > > best, > > Gerrit > > > Message: 5 > Date: Tue, 26 Apr 2016 22:39:22 +0700 > From: andrian <andrian.c...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] LINCS warning of QMMM simulation > Message-ID: <571f8baa.30...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear gromacs users > > i was trying to simulate simple QMMM of 2-chlorobutanol versus > protonated water... my simulation was going well until LINCS warning > appeared. > > "Step 34, time 0.017 (ps) LINCS WARNING relative constraint deviation > after LINCS: rms 0.133339, max 0.231421 (between atoms 2 and 6) bonds > that rotated more than 30 degrees" > > i dont know whats the problem with the system or mdp setting... > > any kind of help is really appreciated... thank you > > cheers > > ************************* > here is my mdp file > title = my_mdp_file > cpp = /lib/cpp > include = > define = > > integrator = md > tinit = 0 > dt = 0.0005 > nsteps = 1000 ; 2ps > nstcomm = 10 > comm_grps = system > > nstxout = 10 > nstvout = 10 > nstfout = 10 > nstlog = 10 > nstenergy = 10 > nstcalcenergy = 10 > nstxtcout = 10 > xtc_grps = system > energygrps = QMatoms MMatoms > > nstlist = 10 > ns_type = grid > pbc = xyz > rlist = 1 > > coulombtype = Reaction-Field > rcoulomb = 1 > epsilon_r = 1 > epsilon_rf = 50 > vdwtype = cut-off > rvdw = 1 > fourierspacing = 0.12 > pme-order = 4 > ewald-rtol = 1e-5 > couple-intramol = no > > tcoupl = v-rescale > tc-grps = MMatoms QMatoms > tau_t = 0.1 0 ; uncoupled QM atoms > ref_t = 300 300 > pcoupl = Berendsen > pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > > QMMM = yes > QMMM-grps = QMatoms > QMmethod = RHF > QMbasis = STO-3G > QMMMscheme = normal > QMcharge = 1 > QMmult = 1 > > gen_vel = no > gen_temp = 300 > gen_seed = 173529 > > constraints = all-bonds > constraint_algorithm = LINCS > continuation = no > shake_sor = no > shake_tol = 0.0005 > lincs_order = 4 > lincs_iter = 1 > lincs_warnangle = 30 > morse = no > ************************************************* > > *********************************************** > here is my topol.top > > ; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > ; Include alkohol_GMX.itp topology > #include "alkohol.acpype/alkohol_GMX.itp" > > ; Include Position restraint file > #ifdef POSRES_ALKOHOL > #include "posre_alkohol.itp" > #endif > > #include "waterH.acpype/waterH_GMX.itp" > > ; Include Position restraint file > #ifdef POSRES_WATER > #include "posre_water.itp" > #endif > > [ system ] > alkohol > > [ molecules ] > ; Compound nmols > alkohol 1 > waterH 1 > ************************************ > > ***************************************** > here is my alkohol itp file > > ; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016 > > [ atomtypes ] > ;name bond_type at.num mass charge ptype sigma > epsilon Amb > c3 c3 6 0.00000 0.00000 A 3.39967e-01 4.57730e-01 > ; 1.91 0.1094 > h1 h1 1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 > ; 1.39 0.0157 > oh oh 8 0.00000 0.00000 A 3.06647e-01 8.80314e-01 > ; 1.72 0.2104 > cl cl 17 0.00000 0.00000 A 3.47094e-01 1.10876e+00 > ; 1.95 0.2650 > hc hc 1 0.00000 0.00000 A 2.64953e-01 6.56888e-02 > ; 1.49 0.0157 > ho ho 1 0.00000 0.00000 A 0.00000e+00 0.00000e+00 > ; 0.00 0.0000 > LA LA 1 0.00000 0.00000 A 0.000000+00 0.00000e+00 > > [ moleculetype ] > ;name nrexcl > alkohol 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass ; qtot > bond_type > 1 c3 1 UNL C 1 0.122400 12.01000 ; qtot 0.122 > 2 c3 1 UNL C1 2 0.015700 12.01000 ; qtot 0.138 > 3 h1 1 UNL H 3 0.058200 1.00800 ; qtot 0.196 > 4 oh 1 UNL O 4 -0.593801 16.00000 ; qtot -0.398 > 5 h1 1 UNL H1 5 0.058200 1.00800 ; qtot -0.339 > 6 c3 1 UNL C2 6 -0.083400 12.01000 ; qtot -0.423 > 7 h1 1 UNL H2 7 0.086700 1.00800 ; qtot -0.336 > 8 cl 1 UNL CL 8 -0.208400 35.45000 ; qtot -0.544 > 9 c3 1 UNL C3 9 -0.097100 12.01000 ; qtot -0.642 > 10 hc 1 UNL H3 10 0.053700 1.00800 ; qtot -0.588 > 11 hc 1 UNL H4 11 0.053700 1.00800 ; qtot -0.534 > 12 hc 1 UNL H5 12 0.041700 1.00800 ; qtot -0.492 > 13 hc 1 UNL H6 13 0.041700 1.00800 ; qtot -0.451 > 14 hc 1 UNL H7 14 0.041700 1.00800 ; qtot -0.409 > 15 ho 1 UNL H8 15 0.409000 1.00800 ; qtot 0.000 > 16 LA 1 UNL LA 16 0.000000 0.00000 > > [ bonds ] > ; ai aj funct r k > 1 2 5 ; 1.5350e-01 2.5363e+05 ; C - C1 > 1 3 5 ; 1.0930e-01 2.8108e+05 ; C - H > 1 4 5 ; 1.4260e-01 2.6284e+05 ; C - O > 1 5 5 ; 1.0930e-01 2.8108e+05 ; C - H1 > 2 6 1 1.5350e-01 2.5363e+05 ; C1 - C2 > 2 7 5 ; 1.0930e-01 2.8108e+05 ; C1 - H2 > 2 8 5 ; 1.7860e-01 2.3347e+05 ; C1 - CL > 4 15 5 ; 9.7400e-02 3.0928e+05 ; O - H8 > 6 9 1 1.5350e-01 2.5363e+05 ; C2 - C3 > 6 10 1 1.0920e-01 2.8225e+05 ; C2 - H3 > 6 11 1 1.0920e-01 2.8225e+05 ; C2 - H4 > 9 12 1 1.0920e-01 2.8225e+05 ; C3 - H5 > 9 13 1 1.0920e-01 2.8225e+05 ; C3 - H6 > 9 14 1 1.0920e-01 2.8225e+05 ; C3 - H7 > > [ pairs ] > ; ai aj funct > 1 9 1 ; C - C3 > 1 10 1 ; C - H3 > 1 11 1 ; C - H4 > 2 12 1 ; C1 - H5 > 2 13 1 ; C1 - H6 > 2 14 1 ; C1 - H7 > 2 15 1 ; C1 - H8 > 3 6 1 ; H - C2 > 3 7 1 ; H - H2 > 3 8 1 ; H - CL > 3 15 1 ; H - H8 > 4 6 1 ; O - C2 > 4 7 1 ; O - H2 > 4 8 1 ; O - CL > 5 6 1 ; H1 - C2 > 5 7 1 ; H1 - H2 > 5 8 1 ; H1 - CL > 5 15 1 ; H1 - H8 > 7 9 1 ; H2 - C3 > 7 10 1 ; H2 - H3 > 7 11 1 ; H2 - H4 > 8 9 1 ; CL - C3 > 8 10 1 ; CL - H3 > 8 11 1 ; CL - H4 > 10 12 1 ; H3 - H5 > 10 13 1 ; H3 - H6 > 10 14 1 ; H3 - H7 > 11 12 1 ; H4 - H5 > 11 13 1 ; H4 - H6 > 11 14 1 ; H4 - H7 > > [ angles ] > ; ai aj ak funct theta cth > 1 2 6 1 1.1063e+02 5.2894e+02 ; C - > C1 - C2 > 1 2 7 1 1.1007e+02 3.8794e+02 ; C - > C1 - H2 > 1 2 8 1 1.1033e+02 4.8409e+02 ; C - > C1 - CL > 1 4 15 1 1.0816e+02 3.9405e+02 ; C - > O - H8 > 2 1 3 1 1.1007e+02 3.8794e+02 ; C1 - > C - H > 2 1 4 1 1.0943e+02 5.6668e+02 ; C1 - > C - O > 2 1 5 1 1.1007e+02 3.8794e+02 ; C1 - > C - H1 > 2 6 9 1 1.1063e+02 5.2894e+02 ; C1 - > C2 - C3 > 2 6 10 1 1.1005e+02 3.8802e+02 ; C1 - > C2 - H3 > 2 6 11 1 1.1005e+02 3.8802e+02 ; C1 - > C2 - H4 > 3 1 4 1 1.0988e+02 4.2652e+02 ; H - > C - O > 3 1 5 1 1.0955e+02 3.2786e+02 ; H - > C - H1 > 4 1 5 1 1.0988e+02 4.2652e+02 ; O - > C - H1 > 6 2 7 1 1.1007e+02 3.8794e+02 ; C2 - > C1 - H2 > 6 2 8 1 1.1033e+02 4.8409e+02 ; C2 - > C1 - CL > 6 9 12 1 1.1005e+02 3.8802e+02 ; C2 - > C3 - H5 > 6 9 13 1 1.1005e+02 3.8802e+02 ; C2 - > C3 - H6 > 6 9 14 1 1.1005e+02 3.8802e+02 ; C2 - > C3 - H7 > 7 2 8 1 1.0593e+02 3.4024e+02 ; H2 - > C1 - CL > 9 6 10 1 1.1005e+02 3.8802e+02 ; C3 - > C2 - H3 > 9 6 11 1 1.1005e+02 3.8802e+02 ; C3 - > C2 - H4 > 10 6 11 1 1.0835e+02 3.2995e+02 ; H3 - > C2 - H4 > 12 9 13 1 1.0835e+02 3.2995e+02 ; H5 - > C3 - H6 > 12 9 14 1 1.0835e+02 3.2995e+02 ; H5 - > C3 - H7 > 13 9 14 1 1.0835e+02 3.2995e+02 ; H6 - > C3 - H7 > > [ dihedrals ] ; propers > ; treated as RBs in GROMACS to use combine multiple AMBER torsions per > quartet > ; i j k l func C0 C1 C2 > C3 C4 C5 > 1 2 6 9 3 3.68192 3.09616 -2.09200 > -3.01248 0.00000 0.00000 ; C- C1- C2- C3 > 1 2 6 10 3 0.66944 2.00832 0.00000 > -2.67776 0.00000 0.00000 ; C- C1- C2- H3 > 1 2 6 11 3 0.66944 2.00832 0.00000 > -2.67776 0.00000 0.00000 ; C- C1- C2- H4 > 2 1 4 15 3 1.71544 0.96232 0.00000 > -2.67776 0.00000 0.00000 ; C1- C- O- H8 > 2 6 9 12 3 0.66944 2.00832 0.00000 > -2.67776 0.00000 0.00000 ; C1- C2- C3- H5 > 2 6 9 13 3 0.66944 2.00832 0.00000 > -2.67776 0.00000 0.00000 ; C1- C2- C3- H6 > 2 6 9 14 3 0.66944 2.00832 0.00000 > -2.67776 0.00000 0.00000 ; C1- C2- C3- H7 > 3 1 2 6 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H- C- C1- C2 > 3 1 2 7 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H- C- C1- H2 > 3 1 2 8 3 1.04600 -1.04600 0.00000 > 0.00000 0.00000 0.00000 ; H- C- C1- CL > 3 1 4 15 3 0.69733 2.09200 0.00000 > -2.78933 0.00000 0.00000 ; H- C- O- H8 > 4 1 2 6 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; O- C- C1- C2 > 4 1 2 7 3 1.04600 -1.04600 0.00000 > 0.00000 0.00000 0.00000 ; O- C- C1- H2 > 4 1 2 8 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; O- C- C1- CL > 5 1 2 6 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H1- C- C1- C2 > 5 1 2 7 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H1- C- C1- H2 > 5 1 2 8 3 1.04600 -1.04600 0.00000 > 0.00000 0.00000 0.00000 ; H1- C- C1- CL > 5 1 4 15 3 0.69733 2.09200 0.00000 > -2.78933 0.00000 0.00000 ; H1- C- O- H8 > 7 2 6 9 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H2- C1- C2- C3 > 7 2 6 10 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H2- C1- C2- H3 > 7 2 6 11 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; H2- C1- C2- H4 > 8 2 6 9 3 0.65084 1.95253 0.00000 > -2.60338 0.00000 0.00000 ; CL- C1- C2- C3 > 8 2 6 10 3 1.04600 -1.04600 0.00000 > 0.00000 0.00000 0.00000 ; CL- C1- C2- H3 > 8 2 6 11 3 1.04600 -1.04600 0.00000 > 0.00000 0.00000 0.00000 ; CL- C1- C2- H4 > 10 6 9 12 3 0.62760 1.88280 0.00000 > -2.51040 0.00000 0.00000 ; H3- C2- C3- H5 > 10 6 9 13 3 0.62760 1.88280 0.00000 > -2.51040 0.00000 0.00000 ; H3- C2- C3- H6 > 10 6 9 14 3 0.62760 1.88280 0.00000 > -2.51040 0.00000 0.00000 ; H3- C2- C3- H7 > 11 6 9 12 3 0.62760 1.88280 0.00000 > -2.51040 0.00000 0.00000 ; H4- C2- C3- H5 > 11 6 9 13 3 0.62760 1.88280 0.00000 > -2.51040 0.00000 0.00000 ; H4- C2- C3- H6 > 11 6 9 14 3 0.62760 1.88280 0.00000 > -2.51040 0.00000 0.00000 ; H4- C2- C3- H7 > > [ virtual_sites2 ] > 16 2 6 1 0.65 > > [ constraints ] > 2 6 2 0.153 > ************************************************************************************************************** > here is my protonated water itp file > ; waterH_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:17 2016 > > [ moleculetype ] > ;name nrexcl > waterH 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass ; qtot > bond_type > 1 oh 1 HOH O 1 -0.710002 16.00000 ; qtot -0.710 > 2 ho 1 HOH H 2 0.570001 1.00800 ; qtot -0.140 > 3 ho 1 HOH H1 3 0.570001 1.00800 ; qtot 0.430 > 4 ho 1 HOH H2 4 0.570001 1.00800 ; qtot 1.000 > > [ bonds ] > ; ai aj funct r k > 1 2 5 ; 9.7400e-02 3.0928e+05 ; O - H > 1 3 5 ; 9.7400e-02 3.0928e+05 ; O - H1 > 1 4 5 ; 9.7400e-02 3.0928e+05 ; O - H2 > > [ angles ] > ; ai aj ak funct theta cth > 2 1 3 1 1.0480e+02 3.5087e+02 ; H - > O - H1 > 2 1 4 1 1.0480e+02 3.5087e+02 ; H - > O - H2 > 3 1 4 1 1.0480e+02 3.5087e+02 ; H1 - > O - H2 > ************************************************************************* > > ********************************************************************** > here is my ORCAINFO file > ! AM1 OPT tightSCF > ! PModel # Initial density Guess > ! XYZFile # Type of Coordinates > > %scf > SCFMode Direct > MaxIter 1500 > UseCheapInts true > end > ************************************************** > > > > -- > Andrian Saputra > Department of Pharmaceutical Science > Sumatera Institute of Technology, Indonesia > > > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 144, Issue 151 > ******************************************************* -- Andrian Saputra Department of Pharmaceutical Science Sumatera Institute of Technology, Indonesia -------------- next part -------------- ; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016 [ atomtypes ] ;name bond_type at.num mass charge ptype sigma epsilon Amb c3 c3 6 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 h1 h1 1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 oh oh 8 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 cl cl 17 0.00000 0.00000 A 3.47094e-01 1.10876e+00 ; 1.95 0.2650 hc hc 1 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 ho ho 1 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 LA LA 1 0.00000 0.00000 A 0.000000+00 0.00000e+00 [ moleculetype ] ;name nrexcl alkohol 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 c3 1 UNL C 1 0.122400 12.01000 ; qtot 0.122 2 c3 1 UNL C1 2 0.015700 12.01000 ; qtot 0.138 3 h1 1 UNL H 3 0.058200 1.00800 ; qtot 0.196 4 oh 1 UNL O 4 -0.593801 16.00000 ; qtot -0.398 5 h1 1 UNL H1 5 0.058200 1.00800 ; qtot -0.339 6 c3 1 UNL C2 6 -0.083400 12.01000 ; qtot -0.423 7 h1 1 UNL H2 7 0.086700 1.00800 ; qtot -0.336 8 cl 1 UNL CL 8 -0.208400 35.45000 ; qtot -0.544 9 c3 1 UNL C3 9 -0.097100 12.01000 ; qtot -0.642 10 hc 1 UNL H3 10 0.053700 1.00800 ; qtot -0.588 11 hc 1 UNL H4 11 0.053700 1.00800 ; qtot -0.534 12 hc 1 UNL H5 12 0.041700 1.00800 ; qtot -0.492 13 hc 1 UNL H6 13 0.041700 1.00800 ; qtot -0.451 14 hc 1 UNL H7 14 0.041700 1.00800 ; qtot -0.409 15 ho 1 UNL H8 15 0.409000 1.00800 ; qtot 0.000 16 LA 1 UNL LA 16 0.000000 0.00000 [ bonds ] ; ai aj funct r k 1 2 5 ; 1.5350e-01 2.5363e+05 ; C - C1 1 3 5 ; 1.0930e-01 2.8108e+05 ; C - H 1 4 5 ; 1.4260e-01 2.6284e+05 ; C - O 1 5 5 ; 1.0930e-01 2.8108e+05 ; C - H1 2 6 1 1.5350e-01 2.5363e+05 ; C1 - C2 2 7 5 ; 1.0930e-01 2.8108e+05 ; C1 - H2 2 8 5 ; 1.7860e-01 2.3347e+05 ; C1 - CL 4 15 5 ; 9.7400e-02 3.0928e+05 ; O - H8 6 9 1 1.5350e-01 2.5363e+05 ; C2 - C3 6 10 1 1.0920e-01 2.8225e+05 ; C2 - H3 6 11 1 1.0920e-01 2.8225e+05 ; C2 - H4 9 12 1 1.0920e-01 2.8225e+05 ; C3 - H5 9 13 1 1.0920e-01 2.8225e+05 ; C3 - H6 9 14 1 1.0920e-01 2.8225e+05 ; C3 - H7 [ pairs ] ; ai aj funct 1 9 1 ; C - C3 1 10 1 ; C - H3 1 11 1 ; C - H4 2 12 1 ; C1 - H5 2 13 1 ; C1 - H6 2 14 1 ; C1 - H7 2 15 1 ; C1 - H8 3 6 1 ; H - C2 3 7 1 ; H - H2 3 8 1 ; H - CL 3 15 1 ; H - H8 4 6 1 ; O - C2 4 7 1 ; O - H2 4 8 1 ; O - CL 5 6 1 ; H1 - C2 5 7 1 ; H1 - H2 5 8 1 ; H1 - CL 5 15 1 ; H1 - H8 7 9 1 ; H2 - C3 7 10 1 ; H2 - H3 7 11 1 ; H2 - H4 8 9 1 ; CL - C3 8 10 1 ; CL - H3 8 11 1 ; CL - H4 10 12 1 ; H3 - H5 10 13 1 ; H3 - H6 10 14 1 ; H3 - H7 11 12 1 ; H4 - H5 11 13 1 ; H4 - H6 11 14 1 ; H4 - H7 [ angles ] ; ai aj ak funct theta cth 1 2 6 1 1.1063e+02 5.2894e+02 ; C - C1 - C2 1 2 7 1 1.1007e+02 3.8794e+02 ; C - C1 - H2 1 2 8 1 1.1033e+02 4.8409e+02 ; C - C1 - CL 1 4 15 1 1.0816e+02 3.9405e+02 ; C - O - H8 2 1 3 1 1.1007e+02 3.8794e+02 ; C1 - C - H 2 1 4 1 1.0943e+02 5.6668e+02 ; C1 - C - O 2 1 5 1 1.1007e+02 3.8794e+02 ; C1 - C - H1 2 6 9 1 1.1063e+02 5.2894e+02 ; C1 - C2 - C3 2 6 10 1 1.1005e+02 3.8802e+02 ; C1 - C2 - H3 2 6 11 1 1.1005e+02 3.8802e+02 ; C1 - C2 - H4 3 1 4 1 1.0988e+02 4.2652e+02 ; H - C - O 3 1 5 1 1.0955e+02 3.2786e+02 ; H - C - H1 4 1 5 1 1.0988e+02 4.2652e+02 ; O - C - H1 6 2 7 1 1.1007e+02 3.8794e+02 ; C2 - C1 - H2 6 2 8 1 1.1033e+02 4.8409e+02 ; C2 - C1 - CL 6 9 12 1 1.1005e+02 3.8802e+02 ; C2 - C3 - H5 6 9 13 1 1.1005e+02 3.8802e+02 ; C2 - C3 - H6 6 9 14 1 1.1005e+02 3.8802e+02 ; C2 - C3 - H7 7 2 8 1 1.0593e+02 3.4024e+02 ; H2 - C1 - CL 9 6 10 1 1.1005e+02 3.8802e+02 ; C3 - C2 - H3 9 6 11 1 1.1005e+02 3.8802e+02 ; C3 - C2 - H4 10 6 11 1 1.0835e+02 3.2995e+02 ; H3 - C2 - H4 12 9 13 1 1.0835e+02 3.2995e+02 ; H5 - C3 - H6 12 9 14 1 1.0835e+02 3.2995e+02 ; H5 - C3 - H7 13 9 14 1 1.0835e+02 3.2995e+02 ; H6 - C3 - H7 [ dihedrals ] ; propers ; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet ; i j k l func C0 C1 C2 C3 C4 C5 1 2 6 9 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ; C- C1- C2- C3 1 2 6 10 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; C- C1- C2- H3 1 2 6 11 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; C- C1- C2- H4 2 1 4 15 3 1.71544 0.96232 0.00000 -2.67776 0.00000 0.00000 ; C1- C- O- H8 2 6 9 12 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; C1- C2- C3- H5 2 6 9 13 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; C1- C2- C3- H6 2 6 9 14 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; C1- C2- C3- H7 3 1 2 6 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H- C- C1- C2 3 1 2 7 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H- C- C1- H2 3 1 2 8 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; H- C- C1- CL 3 1 4 15 3 0.69733 2.09200 0.00000 -2.78933 0.00000 0.00000 ; H- C- O- H8 4 1 2 6 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; O- C- C1- C2 4 1 2 7 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; O- C- C1- H2 4 1 2 8 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; O- C- C1- CL 5 1 2 6 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H1- C- C1- C2 5 1 2 7 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H1- C- C1- H2 5 1 2 8 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; H1- C- C1- CL 5 1 4 15 3 0.69733 2.09200 0.00000 -2.78933 0.00000 0.00000 ; H1- C- O- H8 7 2 6 9 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H2- C1- C2- C3 7 2 6 10 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H2- C1- C2- H3 7 2 6 11 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; H2- C1- C2- H4 8 2 6 9 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CL- C1- C2- C3 8 2 6 10 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; CL- C1- C2- H3 8 2 6 11 3 1.04600 -1.04600 0.00000 0.00000 0.00000 0.00000 ; CL- C1- C2- H4 10 6 9 12 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; H3- C2- C3- H5 10 6 9 13 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; H3- C2- C3- H6 10 6 9 14 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; H3- C2- C3- H7 11 6 9 12 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; H4- C2- C3- H5 11 6 9 13 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; H4- C2- C3- H6 11 6 9 14 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; H4- C2- C3- H7 [ virtual_sites2 ] 16 2 6 1 0.65 [ constraints ] 2 6 2 0.153 -------------- next part -------------- ; waterH_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:17 2016 [ moleculetype ] ;name nrexcl waterH 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 oh 1 HOH O 1 -0.710002 16.00000 ; qtot -0.710 2 ho 1 HOH H 2 0.570001 1.00800 ; qtot -0.140 3 ho 1 HOH H1 3 0.570001 1.00800 ; qtot 0.430 4 ho 1 HOH H2 4 0.570001 1.00800 ; qtot 1.000 [ bonds ] ; ai aj funct r k 1 2 5 ; 9.7400e-02 3.0928e+05 ; O - H 1 3 5 ; 9.7400e-02 3.0928e+05 ; O - H1 1 4 5 ; 9.7400e-02 3.0928e+05 ; O - H2 [ angles ] ; ai aj ak funct theta cth 2 1 3 1 1.0480e+02 3.5087e+02 ; H - O - H1 2 1 4 1 1.0480e+02 3.5087e+02 ; H - O - H2 3 1 4 1 1.0480e+02 3.5087e+02 ; H1 - O - H2 -------------- next part -------------- Grunge ROck MAChoS 20 1UNL C 1 2.600 2.380 2.439 1UNL C1 2 2.540 2.521 2.421 1UNL H 3 2.554 2.304 2.376 1UNL O 4 2.587 2.339 2.575 1UNL H1 5 2.708 2.376 2.422 1UNL C2 6 2.388 2.522 2.440 1UNL H2 7 2.554 2.559 2.319 1UNL CL 8 2.612 2.651 2.519 1UNL C3 9 2.327 2.649 2.379 1UNL H3 10 2.363 2.497 2.543 1UNL H4 11 2.354 2.441 2.375 1UNL H5 12 2.287 2.725 2.447 1UNL H6 13 2.241 2.628 2.315 1UNL H7 14 2.400 2.708 2.323 1UNL H8 15 2.565 2.244 2.568 1UNL LA 16 2.464 2.521 2.430 2HOH O 17 2.592 2.475 2.796 2HOH H 18 2.684 2.494 2.769 2HOH H1 19 2.589 2.419 2.716 2HOH H2 20 2.560 2.560 2.760 5.00000 5.00000 5.00000 -------------- next part -------------- ; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 ; Include alkohol_GMX.itp topology #include "alkohol.acpype/alkohol_GMX.itp" ; Include Position restraint file #ifdef POSRES_ALKOHOL #include "posre_alkohol.itp" #endif #include "waterH.acpype/waterH_GMX.itp" ; Include Position restraint file #ifdef POSRES_WATER #include "posre_water.itp" #endif [ system ] alkohol [ molecules ] ; Compound nmols alkohol 1 waterH 1 -------------- next part -------------- [ System ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 [ Other ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 [ UNL ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 [ Water ] 17 18 19 20 [ SOL ] 17 18 19 20 [ non-Water ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 [ QMatoms ] 1 2 3 4 5 7 8 15 16 17 18 19 20 [ MMatoms ] 6 9 10 11 12 13 14 -------------- next part -------------- ! AM1 OPT tightSCF ! PModel # Initial density Guess ! XYZFile # Type of Coordinates %scf SCFMode Direct MaxIter 1500 UseCheapInts true end -------------- next part -------------- title = my_mdp_file cpp = /lib/cpp include = define = integrator = md tinit = 0 dt = 0.0005 nsteps = 1000 ; 2ps nstcomm = 10 comm_grps = system nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstcalcenergy = 10 nstxtcout = 10 xtc_grps = system energygrps = QMatoms MMatoms nstlist = 10 ns_type = grid pbc = xyz rlist = 1 coulombtype = Reaction-Field rcoulomb = 1 epsilon_r = 1 epsilon_rf = 50 vdwtype = cut-off rvdw = 1 fourierspacing = 0.12 pme-order = 4 ewald-rtol = 1e-5 couple-intramol = no tcoupl = v-rescale tc-grps = MMatoms QMatoms tau_t = 0.1 0 ; QM atoms are uncoupled ref_t = 300 300 pcoupl = Berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 QMMM = yes QMMM-grps = QMatoms QMmethod = RHF QMbasis = STO-3G QMMMscheme = ONIOM QMcharge = 1 QMmult = 1 gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS continuation = no shake_sor = no shake_tol = 0.0005 lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 morse = no ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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