hi i am trying to run mdrun for protein in membrane system. When i run mdrun i get a warning
Step -2, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2.144082 (between atoms 12433 and 12434) rms 0.216090 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11761 11762 90.0 0.1633 0.2387 0.1000 11929 11930 31.7 0.1633 0.1000 0.1000 12097 12098 90.0 0.1632 0.1041 0.1000 12265 12266 90.0 0.1633 0.2266 0.1000 12433 12434 90.0 0.1633 0.3144 0.1000 starting mdrun 'alamethicin in popc' 500 steps, 0.5 ps. Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is larger t han the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 12007 and 12008) rms inf bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 11619 11620 90.0 0.1000 0.1411 0.1000 11633 11634 90.0 0.1000 13155507200.0000 0.1000 11640 11641 90.0 0.1000 0.1214 0.1000 ..... 12619 12620 90.0 0.1080 0.1447 0.1080 Wrote pdb files with previous and current coordinates step 0Segmentation fault I am using shake in my mdp file. I want to restrain water. my mdp file is: title = popc128a integrator = md define = -DFLEX_SPC dt = 0.001 nsteps = 500 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.0 nstlist = 10.0 Tcoupl = no pcoupl = no compressibility = 4.5e-5 gen_temp = 300 gen_vel = no Please help. Thanks in advance. _________________________________________________________________ Check out some new online services at Windows Live Ideas—so new they haven’t even been officially released yet. http://www.msnspecials.in/windowslive/_______________________________________________ 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