Hi there, I am running gromacs in parellel with mpi interface..(np 20) but it is exiting with the following error in output file . . . .Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.151530 (between atoms 2685 and 2686) rms 0.187095 bonds that rotated more than 30 degrees: . . . . Wrote pdb files with previous and current coordinates srun: error: n26: task3: Segmentation fault srun: Terminating job
I am not understanding the error, Can anybody help me in understanding that what does this error indicates ? following is the md.mdp file I am using to run simulation. Is there any problem with the parameters ? md.mdp.............................................. title = trp_drg MD cpp = /lib/cpp ; location of cpp on SGI constraints = all-bonds integrator = md dt = 0.02 ; ps ! nsteps = 250000 ; total 5000 ps. nstcomm = 1 nstxout = 25000 ; output coordinates every 500.0 ps nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = protein NDP sol ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Any suggestion would be of great help.. With Thanks, Vivek
_______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
