[gmx-users] Problems with metals GROMACS/CPMD

[jorge_quintero at ciencias.uis.edu.co]

Hello all.

I have tried to perfomed some simulations about protein dynamics, including
one copper ion around the protein by Gromacs/CPMD.  However, I get
some problems during CPMD simulation.

In the *.mdp file I added the following:
------------------------------------------------------------------------
QMMM                =  yes
QMmethod            =  CPMD
QMMMscheme          =  normal
QMMM-grps           =  QM
QMbasis             =  STO-3G
planewavecutoff     =  40
qmmmcoul_cutoff     =  40
qmbox_cpmd          =  40.0 40.0 40.0
; QM charge
QMcharge                 = 2
; QM multiplicity
QMmult                   = 1
; Surface Hopping
------------------------------------------------------------------------

In the CPMD_inp.tmpl file I added:

&CPMD
   INTERFACE GMX
   MOLECULE CENTER OFF
&END

&DFT
  FUNCTIONAL LDA
&END

&SYSTEM
   SYMMETRY
   0
   CELL
   30.0 1.0 1.0 0.0 0.0 0.0
   CUTOFF
   110.0
   CHARGE
   2
&END

&ATOMS
*H_VDB.uspp BINARY NEWF TPSEU
 LMAX=S
*C_VDB.uspp BINARY NEWF TPSEU
  LMAX=P
*O_VDB.uspp BINARY NEWF TPSEU
  LMAX=P
*N_VDB.uspp BINARY NEWF TPSEU
  LMAX=P
*Cu_VDB.uspp BINARY NEWF TPSEU
  LMAX=D LOCAL=P
&END
---------------------------------------------------------------

During my simulation I get the above message:

 ***************************** ATOMS ****************************
   NR   TYPE        X(bohr)        Y(bohr)        Z(bohr)     MBL
    1      H      21.823587      25.130608      15.200097       3
    2      H      24.280230      24.280222      13.688314       3
    3      H      20.236217      24.223539      11.458441       3
    4      H      22.082445      21.459965      11.112804       3
    5      H      17.140066      21.209700      12.743852       3
    6      H      14.522986      19.494656      19.351984       3
    7      H      15.663084      23.637722      25.007776       3
    8      H      11.751351      25.036116      22.891285       3
    9      H      11.789140      23.581034      18.091379       3
   10      H      24.969240      15.511571      28.327412       3
   11      H      23.656624      18.214203      29.448629       3
   12      H      24.922737      20.670853      25.782564       3
   13      H      26.491213      18.081922      24.459755       3
   14      H      27.596189      19.481304      27.288034       3
   15      H      20.372282      15.476724      27.237070       3
   16      H      21.691307      22.466095      21.492886       3
   17      C      21.011011      22.598375      12.478894       3
   18      C      18.800028      21.181072      13.688314       3
   19      C      15.058371      21.502331      19.338598       3
   20      C      15.133955      22.976320      23.155846       3
   21      C      13.111957      23.127495      19.584265       3
   22      C      24.091259      17.212650      27.710081       3
   23      C      25.924290      18.951195      26.254995       3
   24      C      21.483442      16.815811      26.425072       3
   25      O      19.102385      20.141733      15.767013       3
   26      O      20.840929      18.214203      24.629829       3
   27      N      22.692860      23.562132      14.482003       3
   28      N      16.683536      22.503889      21.190529       3
   29      N      12.998570      23.826700      22.078703       3
   30     Cu      21.011011      22.598375      12.478894       3
   31     Cu      18.800028      21.181072      13.688314       3
   32     Cu      15.058371      21.502331      19.338598       3
   33     Cu      15.133955      22.976320      23.155846       3
   34     Cu      13.111957      23.127495      19.584265       3
   35     Cu      24.091259      17.212650      27.710081       3
   36     Cu      25.924290      18.951195      26.254995       3
   37     Cu      21.483442      16.815811      26.425072       3
 ****************************************************************
 ATOM TYPE=           2  NUM=           1   21.011011100000005
22.598375300000001        12.478894200000001
 ATOM TYPE=           5  NUM=           1   21.011011100000005
22.598375300000001        12.478894200000001


 PROGRAM STOPS IN SUBROUTINE  SETSYS| ATOMS ARE VERY CLOSE
STOP 999
---------------------------------------------------------------

I worked only with one copper, but in the CPMD_inp.run file appears
multiple copper atoms.  Any suggestion about that.  Thanks.