Dear Gmx users,<br> I am trying to do minimization of my system .i have no problem wehen i grompp it but when i do the mdrun its giving me some segmentation error.I had attached the output of grompp and mdrun below.Any suggestions please.Thanks in advance<br>
<font size="4"><b>OUTPUT OF GROMPP</b></font><br><br>Ignoring obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp'<br><br>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>Generated 332520 of the 332520 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'Ion'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>
Analysing residue names:<br>There are: 2 Ion residues<br>There are: 875 Water residues<br>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>Number of degrees of freedom in T-Coupling group rest is 5253.00<br>
Largest charge group radii for Van der Waals: 0.039, 0.039 nm<br>Largest charge group radii for Coulomb: 0.085, 0.085 nm<br>This run will generate roughly 7 Mb of data<br><br>Back Off! I just backed up em.tpr to ./#em.tpr.2#<br>
<br><br><br><br><br><font size="4"><b>OUTPUT OF MDRUN</b></font><br><br>Reading file em.tpr, VERSION 4.5.3 (single precision)<br>Starting 2 threads<br><br>WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential<br>
<br><br>WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the forces deviate on average -2147483648% from minus the numerical derivative of the potential<br><br>Making 1D domain decomposition 2 x 1 x 1<br>
starting mdrun 'NA SODIUM ION in water'<br>10000 steps, 200.0 ps.<br><br>step 0: Water molecule starting at atom 2553 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>
<br>step 0: Water molecule starting at atom 2595 can not be settled.<br>Check for bad contacts and/or reduce the timestep if appropriate.<br>Wrote pdb files with previous and current coordinates<br>Wrote pdb files with previous and current coordinates<br>
Segmentation fault<br><br><font size="4"><b>EM.MDP</b></font><br>title = nacl<br>cpp = /usr/bin/cpp ; the c preprocessor<br>;define= -DEFLEXIBLE<br>integrator = md<br>dt = 0.02 ; ps !<br>nsteps = 10000<br>nstlist = -1<br>
coulombtype = user<br>energygrps = Na Cl Sol<br>energygrp_table = Na Cl<br>vdwtype= user<br>ns_type = grid<br>rlist = 1.4<br>rcoulomb = 1.0<br>rvdw = 1.0<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>
pme_order = 4<br>pbc=xyz;<br>; Energy minimizing stuff<br>emtol = 1000.0<br>emstep = 0.01<br><br>regards,<br>sree<br><br>