[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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