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.
try to "Increase the box size or decrease rlist." <= as ERROR message suggests On 10/9/07, pragya chohan <[EMAIL PROTECTED]> wrote: > > hi... i have been trying to do grompp for the following file but am getting > this error: > There were 1 error(s) processing your input > WARNING 3 [file "popc.top", line 32]: > 7380 non-matching atom names > atom names from popc.top will be used > atom names from popc.pdb will be ignored > 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. > There were 3 warnings > > The grompp command i am using is: > grompp -f 7eq_w.mdp -c popc.pdb -p popc.top -o poc.tpr > > the inputs are: > > popc.mdp > > title = popc128a > integrator = md > define = -DPOSRES -DFLEX_SPC > dt = 0.002 > nsteps = 25000 > nstxout = 500 > ns_type = grid > pbc = xyz > constraints = hbonds > constraints_algorithm= shake > coulombtype = PME > vdwtype = cut-off > rcoloumb = 1.4 > Tcoupl = berendsen > pcoupl = berendsen > tau_t = 0.1 0.1 > tc_grps = POPC SOL > ref_t = 300 300 > ref_p = 1.0 > pcoupltype = isotropic > compressibility = 4.5e-5 > gen_temp = 300 > > popc.top > > #include "ffgmx.itp" > #include "lipid.itp" > #include "popc.itp" > #ifdef FLEX_SPC > #include "flexspc.itp" > #else > #include "spc.itp" > #endif > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > ; Include generic topology for ions > #include "ions.itp" > #ifdef POSRES > #include "lipid_posre.itp" > #endif > [ system ] > ; Name > Pure DPPC bilayer with 128 lipids and 3655 water molecules > [ molecules ] > ; Compound #mols > POPC 128 > SOL 2460 > > > > ________________________________ > Call friends with PC-to-PC calling -- FREE Try it now! > _______________________________________________ > 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 > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. _______________________________________________ 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
