Dear All, Before I start, I have already searched through the mailing list archives, etc...and have energy minimized my structure (s) ;
I get the range check error; _________________________________________________________________________ Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 19683 ] __________________________________________________________________________ does anyone have a fix for this? I have first energy minimized my structures. There are two seperate proteins with two seperate protein domains (chain a,b each) making up two receptors which interact with eachother transiently, or strongly in the presence of a molecule. The two proteins are seperated (manually) by 10 angstroms. I first energy minimized these, then added waters and ions. I had problems with force fields that recognized all the ions (Mg2+, Ca2+, K+, Na+, Cl-) and ended up using the oplsaa force fields. Now, I try an initial run, MD or a simple 100 step energy minimization, prior to a long run, and get the above error again and again. The two scripts mentioned are below inline. I have however played around with everything I could. I have also started from scratch 3 times, ie the initial proteins-minimize-add waters/ions-and then it crashes? Also, does anyone know what the variable "ci" is? Thanks for any help Stephan Watkins ____________________________________________________________ Energy minimize short; title = cpp = define = constraints = none integrator = steep tinit = 0 dt = 0.002 ; ps ! nsteps = 100 init_step = 0 ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.02 ______________________________________________________________ energy minimize long; constraints = all-bonds integrator = cg dt = 0.002 ; ps ! nsteps = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 nstcgsteep = 25 __________________________________________________ and the MD run file; integrator = md dt = 0.005 nsteps = 1000 nstxout = 100000 nstvout = 100000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_grps = system energygrps = system nstlist = 20 coulombtype = PME ns_type = grid rlist = 1.5 rcoulomb = 1.5 rvdw = 1.5 pbc = xyz table-extension = 20 ;Temperature coupling tcoupl = berendsen tc-grps = system tau_t = 1.0 ref_t = 50.0 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 2.01 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = all ;Velocity generation gen_vel = yes gen_temp = 50.0 gen_seed = 30 ld_seed = 130 comm_mode = angular -- Sicherer, schneller und einfacher. Die aktuellen Internet-Browser - jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
