Dear Experts Hello. I have tried to run md simulation with wall option, which included "nwall=2". However, there have been some problems. Always, the running is down with no error message or a message like below. -------------------------------------------------------Program mdrun_mpi_d, VERSION 4.5.3Source code file: ns.c, line: 2544 Fatal error:One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors------------------------------------------------------- And at this point, my triclinic system was getting larger in both Z-directions, and was getting smaller in X and Y directions.In my thinking, it may be happen because of changing the box. Can anyone who have experience like that or how to handle this give me some advise? I attach some parts of my mdp file to run md. ; 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 on pcoupl = Berendsen ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 2.0 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, in bar compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xy ; 2-D PBC ;Wall nwall = 2 ; wall_type = 9-3 wall_r_linpot = 1 wall_atomtype = opls_001 opls_001 wall_density = 20 20 wall_ewald_zfac = 3 ewald_geometry = 3dc ;
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