Could be a result of not setting x/y compressibility = 0 as the manual suggests you should do...
On 2012-09-05 11:28:30AM +0000, 김현식 wrote: > > 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 ; > > > > Thank youHyunsik > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
