hai, to check if my table is correct i just copied the 6-9 table for /share/top to local directory ( to check if the prob is same with any other potential) and grompped it and when i did the mdrun i am still getting the same error.Any suggestions.
On Fri, May 20, 2011 at 6:29 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sreelakshmi ramesh wrote: > >> Dear Gmx users, >> 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 >> *OUTPUT OF GROMPP* >> >> Ignoring obsolete mdp entry 'title' >> Ignoring obsolete mdp entry 'cpp' >> >> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# >> Generated 332520 of the 332520 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 0.5 >> Generated 332520 of the 332520 1-4 parameter combinations >> Excluding 3 bonded neighbours molecule type 'Ion' >> Excluding 2 bonded neighbours molecule type 'SOL' >> Analysing residue names: >> There are: 2 Ion residues >> There are: 875 Water residues >> Analysing residues not classified as Protein/DNA/RNA/Water and splitting >> into groups... >> Number of degrees of freedom in T-Coupling group rest is 5253.00 >> Largest charge group radii for Van der Waals: 0.039, 0.039 nm >> Largest charge group radii for Coulomb: 0.085, 0.085 nm >> This run will generate roughly 7 Mb of data >> >> Back Off! I just backed up em.tpr to ./#em.tpr.2# >> >> >> >> >> >> *OUTPUT OF MDRUN* >> >> Reading file em.tpr, VERSION 4.5.3 (single precision) >> Starting 2 threads >> >> 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 >> >> >> 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 >> >> > These messages indicate that your tables are severely malformed. I suspect > your system is collapsing from an unrealistic physical model. > > -Justin > > > Making 1D domain decomposition 2 x 1 x 1 >> starting mdrun 'NA SODIUM ION in water' >> 10000 steps, 200.0 ps. >> >> step 0: Water molecule starting at atom 2553 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> step 0: Water molecule starting at atom 2595 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> Wrote pdb files with previous and current coordinates >> Wrote pdb files with previous and current coordinates >> Segmentation fault >> >> *EM.MDP* >> title = nacl >> cpp = /usr/bin/cpp ; the c preprocessor >> ;define= -DEFLEXIBLE >> integrator = md >> dt = 0.02 ; ps ! >> nsteps = 10000 >> nstlist = -1 >> coulombtype = user >> energygrps = Na Cl Sol >> energygrp_table = Na Cl >> vdwtype= user >> ns_type = grid >> rlist = 1.4 >> rcoulomb = 1.0 >> rvdw = 1.0 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> pbc=xyz; >> ; Energy minimizing stuff >> emtol = 1000.0 >> emstep = 0.01 >> >> regards, >> sree >> >> > -- > ======================================== > > 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 >
-- 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