Dear Justin, I find:
box (3x3): box[ 0]={ 1.60000e+01, 0.00000e+00, 0.00000e+00} box[ 1]={ 0.00000e+00, 1.60000e+01, 0.00000e+00} box[ 2]={ 0.00000e+00, 0.00000e+00, 1.60000e+01} box_rel (3x3): box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} box_rel[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} boxv (3x3): boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} pres_prev (3x3): pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} svir_prev (3x3): svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fvir_prev (3x3): fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} nosehoover_xi: not available x (2896x3): x[ 0]={-7.49400e+00, 4.57000e-01, 5.00000e-01} x[ 1]={-7.58200e+00, 5.21000e-01, 5.00000e-01} x[ 2]={-7.49600e+00, 3.94000e-01, 4.11000e-01} x[ 3]={-7.49600e+00, 3.94000e-01, 5.89000e-01} x[ 4]={-7.36800e+00, 5.43000e-01, 5.00000e-01} x[ 5]={-7.36800e+00, 6.06000e-01, 5.89000e-01} x[ 6]={-7.36800e+00, 6.06000e-01, 4.11000e-01} x[ 7]={-7.24200e+00, 4.57000e-01, 5.00000e-01} x[ 8]={-7.24200e+00, 3.94000e-01, 4.11000e-01} x[ 9]={-7.24200e+00, 3.94000e-01, 5.89000e-01} x[ 10]={-7.11700e+00, 5.43000e-01, 5.00000e-01} x[ 11]={-7.11700e+00, 6.06000e-01, 5.89000e-01} x[ 12]={-7.11700e+00, 6.06000e-01, 4.11000e-01} x[ 13]={-6.99100e+00, 4.57000e-01, 5.00000e-01} I made box bigger to remove bad contacts in initial configuration (although I have been using the same gro file before and never got such error). Do you recommend I reinstall 4.5.4 ? Appreciate any help... Regards, On 2 June 2011 14:47, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Elisabeth wrote: > >> Hello Justin, >> >> Thank you. I am using >> gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box >> > > You don't need an mdout.mdp file, nor would box vectors be present in one. > What you're looking for is the box information present in the .tpr file. > Run: > > gmxdump -s topol.tpr > out > > Then search in the "out" file for the box information. > > > vector information. This error happens at the very beginning. I see no >> steps are calculated. >> >> > Then the input box information is likely corrupt, or the simulation blows > up at the very start of the simulation (i.e. step 0). > > -Justin > > >> >> On 2 June 2011 13:11, Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Elisabeth wrote: >> >> Hello all, >> >> I am getting the error below at the very beginning of the >> simulation (both serial and parallel). I am sure I did not >> encounter this problem before with the same input files. This >> has just happened now. I really have no clue why this is >> happening. could you please help me? Thank you all in advance. >> >> >> Warning: Only triclinic boxes with the first vector parallel to >> the x-axis and the second vector in the xy-plane are supported. >> Box (3x3): >> Box[ 0]={ nan, 0.00000e+00, 0.00000e+00} >> Box[ 1]={ nan, nan, nan} >> Box[ 2]={ nan, nan, nan} >> Can not fix pbc. >> >> >> Your system is probably blowing up. "Nan" means "not a number," so >> the box vectors have become either infinitely large or small. >> Either the input coordinate file contained a malformed or >> non-existent box, or the simulation is collapsing along the way >> somewhere. Does the simulation run for a while before printing >> this, or is it right away? >> >> You can check the starting box vectors in the .tpr file with gmxdump >> to verify that they are sensible. >> >> -Justin >> >> >> ; 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 = Shift vdw-type >> = Shift rcoulomb-switch = 0 >> rvdw-switch = 0.9 ;0 ; Cut-offs >> rlist = 1.25 rcoulomb >> = 1.0 rvdw = 1.0 ; >> Temperature coupling Tcoupl = v-rescale >> tc-grps = System tau_t >> = 0.1 ref_t = 300 >> ; Pressure coupling >> Pcoupl = Parrinello-Rahman >> Pcoupltype = isotropic tau_p = >> 1 compressibility = 3.5e-5 ref_p >> = 10 ; Velocity generation >> gen_vel = >> yes gen_temp = 300.0 >> gen_seed = 173529 ; Bonds >> constraints = all-bonds >> constraint-algorithm = lincs >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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