hello I am working with protien 1PGB having 56 amino acids (practical tutorial from GROMACS web site) for its simulation using the flexilbe water. the commands that i have run are :
At later stsges of MD simulations ( i.e after position restrained MD), I have been getting few errors which are as follow: --------------------------------------------------------------------------------------------------- *./grompp –f run.mdp –p topol.top –c pr.gro –o run.tpr* followed by *./mdrun –v –deffnm run* 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 .. 486 ] ---------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------- this is my *run.mdp* file integrator = md nsteps = 5000 dt = 0.002 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Berendsen tc-grps = protein non-protein tau-t = 0.1 0.1 ref-t = 298 298 nstxout = 1000 nstvout = 1000 nstxtcout = 100 nstenergy = 100 ---------------------------------------------------------------------------------------------------------------------------- what can i do in order to get rid of this error. your help is kindly needed. In case if i need to give more information, please write back shiny chandy
_______________________________________________ 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
