Dear users, I have done simulation with my protein in water earlier successfully. Now, I am trying to simulate protein in vacum similar to the last simulation of protein-water. When I go to the NPT equilibration, I get a fatal error. The commands I ran:
1.pdb2gmx -f monomer.pdb -o monomer.gro -ter 2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic 3.grompp -f EM.mdp -c monomer_solv_ions.gro -p topol.top -o EM.tpr 4.mdrun -v -deffnm EM Steepest Descents converged to Fmax < 100 in 1632 steps Potential Energy = -2.3169937e+02 Maximum force = 9.9520912e+01 on atom 360 Norm of force = 1.9172571e+01 5.grompp -f NVT.mdp -c EM.gro -p topol.top -o NVT.tpr 6.mdrun -deffnm NVT -v 7.grompp -f NPT.mdp -c NVT.gro -t NVT.cpt -p topol.top -o NPT.tpr 8.mdrun -v -deffnm NPT Fatal error: The X-size of the box (3.202905) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (4) times the smallest allowed cell size (0.800718) The npt.mdp file settings are: ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = Nose-Hoover ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein ; Define groups to be coupled separately to temperature bath tau_t = 0.5 ; Group-wise coupling time constant (ps) ref_t = 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT conditions pcoupltype = isotropic ; Isotropic scaling in the x-y direction, independent of the z direction tau_p = 5.0 ; Coupling time constant (ps) ref_p = 1.0 ; Reference pressure for coupling, x-y, z directions (bar) compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility (bar^-1) refcoord_scaling = com ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = no ; Velocity is read from the previous run ; Centre of mass (COM) motion removal relative to the specified groups nstcomm = 1 ; COM removal frequency (steps) comm_mode = Linear ; Remove COM translation (linear / angular / no) comm_grps = Protein ; COM removal relative to the specified groups Would you please help me? How would it be possible to solve my problem? Thanks in advance. Sincerely, Shima -- 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
