It could be an error in protein structure ( because 1 - 9 interaction ), and we usually overcome similar issues by a pre -energy minimization before submitting to gromacs.
i m carryin a protein explicit solvent simulation using gromacs 3.3 for intially minimizing the hydrogen i did some small mini and equi in the vaccum by maintaing the restraints then i added ions and water but in the very first minimization i m getting the following error 1-4 interaction between 1 and 9 at distance 8.454 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, in the log file im geting : 4 inconsistant shifts check ur topology following is my input file : title = 1min in water define = -DPOSRES integrator = steep dt = 0.001 constraints = none nsteps = 500 nstlist = 10 rcoulomb = 1 rlist = 1 rvdw = 1.4 ns_type = grid coulombtype = PME pbc = xyz gen_vel = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes comm_mode = angular emtol = 100.0 emstep = 0.01 after adding the ions i have modified the topology file, plz tel me what is the exact reason for this error or what are the other things i should check in relation to the error thanks Gurpreet IIT MADRAS -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION BANGALORE INDIA
_______________________________________________ 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
