[gmx-users] Energy minimization with Walls
Hello, I am trying to put together a mdp script for energy minimization using 2 walls in the z direction. I have a slab of just water which is simulated fine if i remove the walls section from the script. when I add the wall section, I start to receive this error "Fatal error: DD cell 4 4 0 could only obtain 19 of the 20 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; My script ; LINES STARTING WITH ';' ARE COMMENTS ;title = Minimization ; Title of run define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force < 1.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform energygrps = system; Which energy group(s) to write to disk nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 pbc = xy; pbc in xy only nwall = 2 ; wall at z=0 and z=z-box wall-type = 10-4 ; direct 12-6 LJ as fn of distance from wall wall-density= 20 20 wall-atomtype = CA CA wall-r-linpot = 1 ewald-geometry = 3dc ; Only Ewald sum compatible with slab geometry, requires box_height >= slab_height * 3 wall-ewald-zfac = 3 ; Extra empty space for slab geometry calculation (reducing coulomb interaction) I hope someone could help me figure what is the problem Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] X2top error, Could only find a forcefield type for 0 out of 66 atoms
Dear Gromacs users, I am trying to transform my PDP file for AL2O3 surface to a top file using x2top. I have defined my forcefield.itp and .n2t file. However, I keep recieving an error telling me that "Could only find a forcefield type for 0 out of 66 atoms" my PDB file looks like COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.2 CRYST14.7598.243 17.151 90.00 90.00 90.00 P1 1 HETATM1 O LIG 1 3.201 0.667 3.490 1.00 0.00 O HETATM2 O LIG 1 0.822 4.789 3.490 1.00 0.00 O HETATM3 O LIG 1 0.822 2.041 7.821 1.00 0.00 O HETATM4 O LIG 1 3.201 6.163 7.821 1.00 0.00 O HETATM5 B LIG 1 3.201 3.415 12.151 1.00 0.00 B HETATM6 B LIG 2 0.822 7.536 12.151 1.00 0.00 B HETATM7 O LIG 1 1.017 1.928 3.490 1.00 0.00 O HETATM8 O LIG 1 3.397 6.050 3.490 1.00 0.00 O HETATM9 O LIG 1 3.397 3.302 7.821 1.00 0.00 O HETATM 10 O LIG 1 1.017 7.424 7.821 1.00 0.00 O my itp file looks like #define _ff_clayff [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.5 [ atomtypes ] ; name mass chargeptype sigma eps ho 1 1.00800 0.4250A0.0e-01 0.0e-01 ;clayFF_hydroxylhydrogen oh 8 15.99800-0.9500A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygen ob 8 15.99800-1.0500A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxyge ao 13 26.98200 1.5750A4.27128e-01 6.0e-06 ;ClayFF_octahedalaluminium [ bondtypes ] ; ij func b0 kb oh ho 10.1000 554134.9 [ angletypes ] ; ijk func th0 cth ao ohho1109.47125.52 my .n2t file looks like B oh -0.950015.998 1H 0.100 ;hydroxyl oxygen O ob -1.299615.998 0 ;bridging oxygen with double substitution H ho -1.080815.998 1B 0.100 ;hydroxyl hydrogen with substitution AL ao1.575026.982 0 ;octahedral aluminium Your help is really appreciated Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
