Dear Gromcas users, I am doing some mutation study, NPT simulations. Initially I was using a generic .mdp file I got from my advisor and I was able to run the systems for ~50ns with out any issues. But then I spend time reading about gromacs and created a .mdp file. However, with my .mdp file the runs are crashing with error: Fatal error: The X-size of the box (4.500406) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (5) times the smallest allowed cell size (0.900000) I understand I can try particle decomposition for this system, but before I want to make sure there is no error in my .mdp file. When I load the trajectory in the vmd, I can see the box is getting compressed too much. The contents of the current .mdp file are shown below. This .mdp file varies from my advisor's for few parameters which I have shown at the end.
contents of my .mdp file: title = Yo cpp = /usr/bin/cpp include = define = integrator = sd tinit = 0.0 dt = 0.002 nsteps = 50000000 nstxout = 1000000 nstvout = 1000000 nstfout = 1000000 nstlog = 10000 nstenergy = 10000 nstxtcout = 10000 xtc_precision = 1000 xtc_grps = energygrps = nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 domain-decomposition = no coulombtype = PME fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 optimize_fft = no epsilon_surface = 0 ewald_geometry = 3d rcoulomb = 0.9 vdwtype = Cut-off rvdw = 0.9 epsilon_r = 1 DispCorr = EnerPres ; with sd as integrator tcoupl is ignored tc-grps = system ; good choice for zeta is 0.5 1/s tau_t = 2.0 ref_t = 310 pcoupl = berendsen pcoupltype = anisotropic nstpcouple = -1 tau_p = 1.0 compressibility = 4.6e-5 4.6e-5 4.6e-5 0 0 0 ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 annealing = no ;annealing_npoints = 3 ;annealing_time = 0 gen_vel = no gen_temp = 310 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS continuation = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 morse = no disre = no disre_weighting = equal disre_mixed = no disre_fc = 1000 disre_tau = 10 nstdisreout = 1000 Parameters that are different in my advisor's file: DispCorr = Ener tau_t = 0.20 compressibility = 5e-6 5e-6 5e-6 0 0 0 gen_vel = yes gen_temp = 1 gen_seed = 473529 I thought when using vdw cutoff, it is recommended to use dispersion corrections for both pressure and energy. Also can some explain the reason behind this? For tau_t, I used 2 as it is the recommended value for sd integrator in the manual. Also gen_vel has to be no for sd integrator, correct? Any help will be appreciated! Thanks in advance, Shyno -- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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