Dear Justin, I made some changes in my .mdp file, but the result is same.
My box size, as mentioned in the previous mail, is 20.1 A. The cut off I used is 8 angstrom. I attach the input file here. ************************************** cpp = /lib/cpp define = -DPOSRES-DFLEX_SPC constraints = none morse = no integrator = steep nsteps = 2000 ; Energy minimizing emtol = 100 emstep = 0.00001 nstcomm = 1 ns_type = grid rlist = 0.8 coulumbtype = pme rcoulomb = 0.8 vdw-type = cut-off rvdw = 0.8 nstenergy = 10 Tcoupl = no Pcoupl = no gen_vel = no ************************************************* And the output message is : --------------------------------------------------------------------------- creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 2 bonded neighbours for SOL 258 NOTE: System has non-zero total charge: -2.580000e-01 processing coordinates... double-checking input for internal consistency... ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. ------------------------------------------------------- Program grompp, VERSION 3.3.2 Source code file: grompp.c, line: 1111 Fatal error: There were 1 error(s) processing your input ------------------------------------------------------- "Stop Drinking My Beer !" (The Amps) ---------------------------------------------------------------------- HOW CAN I SETTLE THIS ISSUE? REGARDS JESTIN
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