Hello, I try to simulate infinite nanotube.
The bonds in topology are as follows: 1 2 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 1 31 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 1 1500 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 2 32 1 1.440000e-01 4.000000e+05 1.440000e-01 4.000000e+05 2 1471 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 3 4 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 3 33 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 3 1472 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 4 34 1 1.440000e-01 4.000000e+05 1.440000e-01 4.000000e+05 4 1473 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 .......................................................................... .......................................................................... The coordinates: 1UNK C 1 2.312 3.095 0.071 1UNK C 2 2.448 3.055 0.071 1UNK C 3 2.698 2.922 0.071 1UNK C 4 2.807 2.831 0.071 1UNK C 5 2.982 2.607 0.071 1UNK C 6 3.044 2.480 0.071 1UNK C 7 3.112 2.205 0.071 1UNK C 8 3.117 2.063 0.071 ............................................ ............................................ 1UNK C 1495 1.305 2.735 6.101 1UNK C 1496 1.511 2.929 6.101 1UNK C 1497 1.633 3.003 6.101 1UNK C 1498 1.900 3.097 6.101 1UNK C 1499 2.041 3.115 6.101 1UNK C 1500 2.323 3.092 6.101 4.20000 4.20000 6.17200 The output of mdrun: Back Off! I just backed up md.log to ./#md.log.2# Getting Loaded... Reading file topol.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'ICE' 1000 steps, 0.0 ps. Segmentation fault The distances between images seem to be correct. pbc=full in mdp. Pressure coupling is off. If one runs x2top without '-pbc' everything is OK. What else can be wrong? Can the below warning lead to the crash (grommp): WARNING 2 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups Checking consistency between energy and charge groups... How to overcome it? Thanks. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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