Quoting [EMAIL PROTECTED]: > Dear gromacs user, > I am doing simulation of Gal1P protein in explicit solvent.when i did > energy minimization of system i got this warning:- > Warning: 1-4 interaction between 2779 and 2788 at distance 1.005 which is > larger than 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.
See here for some general advice: http://wiki.gromacs.org/index.php/blowing_up > > i added table -extention 1.1 in mdp file but i am steel gettingsame > problem.kindly help me. This is probably not the best way to handle the problem. Figure out what the problem is before allowing your system room to explode. How did you prepare the system? Did you make some sort of model that might have bad atomic clashes? What parameters are you using? Are there any ligands/cofactors that you've included that might have been given incorrect parameters? -Justin > i am pasting em.mdp file for your considerartion > thanks in advance. > title = Gal1p > cpp = /lib/cpp > define = -DFLEXIBLE > constraints = none > integrator = steep > dt = 0.002 ; ps ! > nsteps = 50000 > nstlist = 10 > nstcomm = 1 > nstxout = 1000 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.1 > ; > ; Energy minimizing stuff > ; > emtol = 100 > emstep = 0.01 > > > _______________________________________________ > 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
