Hello gmx-users, I am running an NPT simulation with 100 molecules of n-alkane and trying to impose uni-axial pressure of these molecules using semiisotropic option in grompp.mdp. However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message:
------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: ns.c, line: 2295 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. ------------------------------------------------------- I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful. is there any other options in gromacs that I can use to impose uniaxial stress? Or does anyone had any similar problems related to semi-isotropic pressure coupling? Thank you in advance. This is my grompp.mdp file configuration: integrator = md dt = 0.001 ; ps ! nsteps = 1000000 ; nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 vdwtype = switch rvdw = 0.7 rvdw_switch = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; temperature coupling is on Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds ; pressure coupling is on pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 0.5 compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction ref_p = 1.0 1000.0 ;x/y-direction, z-direction -- Yongchul "Greg" Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University
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