On 6/7/18 5:59 AM, Oguz Gurbulak wrote:
Dear Gromacs Users, When I used semiisotropic pressure coupling, I got this error message "Fatal error: The Y-size of the box (4.200315) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (3) times the smallest allowed cell size (1.400000)" Could you please help me to solve this error ?
Your system has become unstable. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
Kind regards. **** MDP FILE **** ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; dt = 0.002 ; ; Output control nstxout = 2000 ; nstvout = 2000 ; nstenergy = 2000 ; nstlog = 2000 ; ; Bond parameters constraint_algorithm = lincs ; constraints = all-bonds ; lincs_iter = 1 ; lincs_order = 4 ; ; Neighbor searching cutoff-scheme = Verlet rlist = 1.4 ; ns_type = grid nstlist = 10 ; nstcomm = 100 ; Electrostatics coulombtype = PME ; rcoulomb = 1.4 ; pme_order = 4 fourierspacing = 0.16 ewald-rtol = 1e-5 ; Dispersion correction DispCorr = EnerPres ; ; Van der Waals vdwtype = cutoff rvdw = 1.4 ; ; Temperature coupling is on tcoupl = V-rescale ; tc-grps = ABC SOL ; tau_t = 0.1 0.1 ; ref_t = 302.7 302.7 ; ; Pressure coupling is on pcoupl = berendsen ; Pressure coupling on in NPT pcoupltype = semiisotropic ; tau_p = 2.0 ; ref_p = 50.0 1.0 ; compressibility = 4.5e-5 4.5e-5 ; ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation continuation = no ; gen_vel = yes ; gen_temp = 302.7 ; gen_seed = -1 ;
-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
