Dear Justin, The nvt.mdp file is:
define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed Are there any something abnormal ? On Mon, Dec 17, 2012 at 8:56 PM, Justin Lemkul <[email protected]> wrote: > > > On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote: > >> Dear All, >> >> I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial. >> After doing step 6 (Do a short energy minimization and position restrained >> simulation),i carry out running NVT equilibrium. But it appears the error >> in the terminal : >> >> Fatal error: >> There is no domain decomposition for 2 nodes that is compatible with the >> given box and a minimum cell size of 5.2375 nm >> Change the number of nodes or mdrun option -rcon or -dds or your LINCS >> settings >> Look in the log file for details on the domain decomposition >> >> What can i do to fix this error ? >> >> > http://www.gromacs.org/**Documentation/Errors#There_is_** > no_domain_decomposition_for_n_**nodes_that_is_compatible_with_** > the_given_box_and_a_minimum_**cell_size_of_x_nm<http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm> > > The fact that the minimum size is over 5 nm is very odd. Are there very > long-range bonded interactions of some sort? Normally the minimum box size > is very close to the value of the longest cutoff unless something abnormal > is present. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
