As far as I am aware, GROMOS53A6 does not play nice with water models other than SPC/E
=================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Pallavi Banerjee <pallavis...@students.iiserpune.ac.in> Sent: Monday, September 14, 2015 9:43 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Using TIP4P(2005) with GROMOS-53a6 Hello users, I am simulating a polymer in TIP4P(2005) water with GROMOS53a6 as the force field. I am using the same mdp options as has been provided in the source website. The following error shows up: " Molecule type 'SOL' has 6 constraints. For stability and efficiency there should not be more constraints than internal number of degrees of freedom: 3 " I tried a sample run with just the water, but the same happens. Could someone provide some valuable insight? Following are the mdp options: ; RUN CONTROL integrator = md nsteps = 500000 dt = 0.001 ; NEIGHBOR SEARCHING cutoff-scheme = Verlet nstlist = 1 ns_type = grid pbc = xyz rlist = 0.85 domain-decomposition = no ; OUTPUT CONTROL nstxout = 10000 nstvout = 10000 nstxtcout =10000 nstlog =1000 nstenergy =1000 ; OPTIONS FOR BONDS = constraints = all-angles ; Type of constraint algorithm = constraint-algorithm = shake ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol = 1e-6 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials = morse = no ; OPTION FOR ELECTROSTATIC AND VDW coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.85 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon_rf = 3.5 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.85 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d ;epsilon_surface = 0 ;optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps = System tau_t = 10 ref_t = 300 Pcoupl = no ;Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 10 compressibility = 5.0e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 Thanks and regards, Pallavi Banerjee. -- 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.
