Check out the wiki at: http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
Alternatively, search the list for some of my posts from around a year ago - NVT and minimization of a lipid bilayer (or search for my name, they should come up as well). I suspect you have bad contacts in your starting structure. -Justin Quoting pragya chohan <[EMAIL PROTECTED]>: > > 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 Ideasso new they havent > 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 > ========================================================= Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ========================================================= _______________________________________________ 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