[gmx-users] Problems with metals GROMACS/CPMD

Pradip Biswas biswas.pk at gmail.com
Sat Sep 19 06:49:30 CEST 2009


Hi, This error has origin in the Gromacs part of the QMMM interface. If you
can send me the index.ndx, .gro, and CPMD_inp.run files, I might figure out
what's going on. -pb.

On Fri, Sep 11, 2009 at 11:38 AM, <jorge_quintero at ciencias.uis.edu.co>wrote:

> 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.
>
>
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-- 
Pradip K Biswas, PhD
Asst. Professor, Department of Physics,
Computational Bioengineering and Nanoscience Group
Tougaloo College, MS 39174
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