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, <[email protected]>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. > > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Pradip K Biswas, PhD Asst. Professor, Department of Physics, Computational Bioengineering and Nanoscience Group Tougaloo College, MS 39174
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