Quoting JMandumpal <[EMAIL PROTECTED]>: > > 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?
Did you read Tsjerk's message from this morning? His suggestions regarding PBC and verifying your box dimensions are good ones that I had not considered. Also note that you probably have a broken topology, as the net charge on your system is non-integral. This has nothing to do with the problem at hand, but it will likely be problematic later. -Justin > > > REGARDS > JESTIN > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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