Hi Saeed, Us a larger box, like edge length 2.5 or 3. The non-matching names are not much of a problem, and you can add -maxwarn 1 to the grompp call.
Cheers, Tsjerk On Apr 2, 2016 8:29 AM, "Saeed Nasiri" <s.t.nas...@gmail.com> wrote: > thank you TsjerkI modified the topology file and did all the thing from the > begnning, but there is another error! > > > > > > *gmx_mpi insert-molecules -ci WATER.pdb -nmol 500 -box 2 2 2 -o > water_box.gro* > ... > ... > ... > > Try 5000 > *Added 392 molecules (out of 500 requested)* > Writing generated configuration to water_box.gro > > Output configuration contains 1176 atoms in 784 residues > ... > ... > > > *******************************************topol.top******************************************************* > ; > #include "oplsaa.ff/forcefield.itp" > ; Include water topology > #include "oplsaa.ff/tip3p.itp" > > > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > [ system ] > A box of water > > [ molecules ] > *SOL 392* > > ************************************************************************************************ > ~/Desktop/water_box $ gmx_mpi grompp -f minim.mdp -c water_box.gro -o > em.tpr -p topol.top > :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par > Bjelkmar > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent > Hindriksen > Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten > Kutzner > Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff > Erik Marklund Teemu Murtola Szilard Pall Sander Pronk > Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers > Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf > and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2015, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS is free software; you can redistribute it and/or modify it > under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > GROMACS: gmx grompp, VERSION 5.1.2 > Executable: /usr/local/gromacs/bin/gmx_mpi > Data prefix: /usr/local/gromacs > Command line: > gmx_mpi grompp -f minim.mdp -c water_box.gro -o em.tpr -p topol.top > > > NOTE 1 [file minim.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > Setting the LD random seed to 26722793 > Generated 330891 of the 330891 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 330891 of the 330891 1-4 parameter combinations > Excluding 2 bonded neighbours molecule type 'SOL' > Warning: atom name 1 in topol.top and water_box.gro does not match (OW - O) > Warning: atom name 2 in topol.top and water_box.gro does not match (HW1 - > H) > Warning: atom name 3 in topol.top and water_box.gro does not match (HW2 - > H) > Warning: atom name 4 in topol.top and water_box.gro does not match (OW - O) > Warning: atom name 5 in topol.top and water_box.gro does not match (HW1 - > H) > Warning: atom name 6 in topol.top and water_box.gro does not match (HW2 - > H) > Warning: atom name 7 in topol.top and water_box.gro does not match (OW - O) > Warning: atom name 8 in topol.top and water_box.gro does not match (HW1 - > H) > Warning: atom name 9 in topol.top and water_box.gro does not match (HW2 - > H) > Warning: atom name 10 in topol.top and water_box.gro does not match (OW - > O) > Warning: atom name 11 in topol.top and water_box.gro does not match (HW1 - > H) > Warning: atom name 12 in topol.top and water_box.gro does not match (HW2 - > H) > Warning: atom name 13 in topol.top and water_box.gro does not match (OW - > O) > Warning: atom name 14 in topol.top and water_box.gro does not match (HW1 - > H) > Warning: atom name 15 in topol.top and water_box.gro does not match (HW2 - > H) > Warning: atom name 16 in topol.top and water_box.gro does not match (OW - > O) > Warning: atom name 17 in topol.top and water_box.gro does not match (HW1 - > H) > Warning: atom name 18 in topol.top and water_box.gro does not match (HW2 - > H) > Warning: atom name 19 in topol.top and water_box.gro does not match (OW - > O) > Warning: atom name 20 in topol.top and water_box.gro does not match (HW1 - > H) > (more than 20 non-matching atom names) > > > > > *WARNING 1 [file topol.top, line 19]: 1176 non-matching atom names atom > names from topol.top will be used atom names from water_box.gro will be > ignored* > > > > > > > *ERROR 1 [file topol.top, line 19]: 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.* > > > Removing all charge groups because cutoff-scheme=Verlet > > > > *There was 1 noteThere was 1 warning* > > ------------------------------------------------------- > Program gmx grompp, VERSION 5.1.2 > Source code file: > /home/nasiri/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 1738 > > > *Fatal error:There was 1 error in input file(s)* > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > Halting program gmx grompp > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > -- > 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. > -- 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.
