Hi, I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (6) times the smallest allowed cell size (1.000605) I also tried to change the number of processors but I got the same error. My system is a protein in vacuo. This is my mdp file (Taken from Justin Lemkul's tutorial for FE calculations: title = NPT equilibration ; Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.002 nsteps = 200000 ; 444400 ps nstcomm = 100 ;Langevin dynamics ld_seed = -1 ; Output control nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 0 xtc-precision = 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist = 1.5 ; Electrostatics coulombtype = PME rcoulomb = 1.5 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t = 1.0 ref_t = 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-05 ref_p = 1.0 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NVT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 Can you please tell my what is wrong? I runned previous nvt, npt and md simulation with the same box size and protein but in water. Is there any way of solving this problem without affecting the accuracy of the simulation? Thank you in advance Sonia Aguilera -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-The-Y-size-of-the-box-times-the-triclinic-skew-factor-is-smaller-than-the-number-of-DD-cells-te-tp5005483.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
