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