dear gromacs user i am doing simulation of Gal1p protein with ligand and without ligand.i made the system without ligand by removing the ligand from pdb file then i use pdb2gmx for generating topology file and editconf for adding box dimention and add spc water molecules.i have not face any problem up to grompp but 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" but em is comleted with machine precession with -ve energy, i added table-extention (1.1nm)in mdp file, and got same warning.even i don't what affect done on system by adding table-extention.I am also getting same problem with ligand.kidnely help me sanjay
itle = 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 [email protected] 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
