On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> Yongchul Chung wrote: > >> 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. >> ------------------------------------------------------- >> > > You're imposing 1000 bar of pressure along the z-axis. Surely you should > expect distortion? > > You should do some maths and work out the expected density of the box under > such pressure. You still need a box large enough that the maximum cut-off > length can be satisfied, so that sets the minimum number of molecules you > need, and thus the initial size of the box. > > Thanks for the input. I should do this. > > I tried all vdwtype options to see whether this would mitigate the issues >> but was unsuccessful. >> > > Don't fool with .mdp settings hoping it'll magically work. Read how they > work, and you might have understood why the minimum image convention > requires that the condition that provoked the above error does not arise. > > Mark > 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 >> >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> > _______________________________________________ > 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/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/mailing_lists/users.php > -- Yongchul "Greg" Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University
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