[gmx-users] simulation a box of water

[Saeed Nasiri]

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 (-:

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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.
--------------------------------------------------------------------------