Hello, I am attempting to increase the density using NPT. As I increase the pressure to compress the system after some steps simulation crashes. I thought maybe its becasue I am compressing too fast but even when I take a stepwise approach to compress gradually the same error comes up. The density at the point of crash is about 30 SI while I need 650 which is the actual density. Topology file is generated successfully and also I did EM before MD.
Initial box size is 30 nm. As suggested in the link below I reduced the size to 20 nm (there are 2500 atoms in the system ) but the same error appears. http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html I also tried less -np from 7 to 4 but no success. Can you please tell me what this exclamation mark mean which I get at times in parallel trials.(vol 0.99 !) Thank you for your time. vol 0.99! imb F 47% step 168000, will finish Fri Mar 4 00:51:29 2011 vol 0.99! imb F 42% step 168100, will finish Fri Mar 4 00:51:26 2011 vol 0.99! imb F 44% step 168200, will finish Fri Mar 4 00:51:30 2011 vol 1.00! imb F 46% step 168300, will finish Fri Mar 4 00:51:27 2011 vol 1.00! imb F 48% step 168400, will finish Fri Mar 4 00:51:25 2011 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec.c, line: 2592 Fatal error: The X-size of the box (5.499734) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (7) times the smallest allowed cell size (0.785678) ======================================== Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec.c, line: 2592 Fatal error: The X-size of the box (4.999741) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.250000) ==================================== pbc = xyz ; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = PME vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ; Cut-offs rlist = 1.25 rcoulomb = 1.25 ;1.1 rvdw = 1.0 ; PME parameters fourierspacing = 0.3 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 400 ;300 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 ;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 8 8 ; Velocity generation gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Bonds constraints = all-bonds constraint-algorithm = lincs
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