<span class="Apple-style-span" style="font-family: 'Lucida Grande'; font-size: 11px; white-space: pre-wrap; ">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.</span><br><br><div class="gmail_quote">On Fri, Sep 11, 2009 at 11:38 AM, <span dir="ltr"><<a href="mailto:jorge_quintero@ciencias.uis.edu.co">jorge_quintero@ciencias.uis.edu.co</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hello all.<br>
<br>
I have tried to perfomed some simulations about protein dynamics, including<br>
one copper ion around the protein by Gromacs/CPMD. However, I get<br>
some problems during CPMD simulation.<br>
<br>
In the *.mdp file I added the following:<br>
------------------------------------------------------------------------<br>
QMMM = yes<br>
QMmethod = CPMD<br>
QMMMscheme = normal<br>
QMMM-grps = QM<br>
QMbasis = STO-3G<br>
planewavecutoff = 40<br>
qmmmcoul_cutoff = 40<br>
qmbox_cpmd = 40.0 40.0 40.0<br>
; QM charge<br>
QMcharge = 2<br>
; QM multiplicity<br>
QMmult = 1<br>
; Surface Hopping<br>
------------------------------------------------------------------------<br>
<br>
In the CPMD_inp.tmpl file I added:<br>
<br>
&CPMD<br>
INTERFACE GMX<br>
MOLECULE CENTER OFF<br>
&END<br>
<br>
&DFT<br>
FUNCTIONAL LDA<br>
&END<br>
<br>
&SYSTEM<br>
SYMMETRY<br>
0<br>
CELL<br>
30.0 1.0 1.0 0.0 0.0 0.0<br>
CUTOFF<br>
110.0<br>
CHARGE<br>
2<br>
&END<br>
<br>
&ATOMS<br>
*H_VDB.uspp BINARY NEWF TPSEU<br>
LMAX=S<br>
*C_VDB.uspp BINARY NEWF TPSEU<br>
LMAX=P<br>
*O_VDB.uspp BINARY NEWF TPSEU<br>
LMAX=P<br>
*N_VDB.uspp BINARY NEWF TPSEU<br>
LMAX=P<br>
*Cu_VDB.uspp BINARY NEWF TPSEU<br>
LMAX=D LOCAL=P<br>
&END<br>
---------------------------------------------------------------<br>
<br>
During my simulation I get the above message:<br>
<br>
***************************** ATOMS ****************************<br>
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL<br>
1 H 21.823587 25.130608 15.200097 3<br>
2 H 24.280230 24.280222 13.688314 3<br>
3 H 20.236217 24.223539 11.458441 3<br>
4 H 22.082445 21.459965 11.112804 3<br>
5 H 17.140066 21.209700 12.743852 3<br>
6 H 14.522986 19.494656 19.351984 3<br>
7 H 15.663084 23.637722 25.007776 3<br>
8 H 11.751351 25.036116 22.891285 3<br>
9 H 11.789140 23.581034 18.091379 3<br>
10 H 24.969240 15.511571 28.327412 3<br>
11 H 23.656624 18.214203 29.448629 3<br>
12 H 24.922737 20.670853 25.782564 3<br>
13 H 26.491213 18.081922 24.459755 3<br>
14 H 27.596189 19.481304 27.288034 3<br>
15 H 20.372282 15.476724 27.237070 3<br>
16 H 21.691307 22.466095 21.492886 3<br>
17 C 21.011011 22.598375 12.478894 3<br>
18 C 18.800028 21.181072 13.688314 3<br>
19 C 15.058371 21.502331 19.338598 3<br>
20 C 15.133955 22.976320 23.155846 3<br>
21 C 13.111957 23.127495 19.584265 3<br>
22 C 24.091259 17.212650 27.710081 3<br>
23 C 25.924290 18.951195 26.254995 3<br>
24 C 21.483442 16.815811 26.425072 3<br>
25 O 19.102385 20.141733 15.767013 3<br>
26 O 20.840929 18.214203 24.629829 3<br>
27 N 22.692860 23.562132 14.482003 3<br>
28 N 16.683536 22.503889 21.190529 3<br>
29 N 12.998570 23.826700 22.078703 3<br>
30 Cu 21.011011 22.598375 12.478894 3<br>
31 Cu 18.800028 21.181072 13.688314 3<br>
32 Cu 15.058371 21.502331 19.338598 3<br>
33 Cu 15.133955 22.976320 23.155846 3<br>
34 Cu 13.111957 23.127495 19.584265 3<br>
35 Cu 24.091259 17.212650 27.710081 3<br>
36 Cu 25.924290 18.951195 26.254995 3<br>
37 Cu 21.483442 16.815811 26.425072 3<br>
****************************************************************<br>
ATOM TYPE= 2 NUM= 1 21.011011100000005<br>
22.598375300000001 12.478894200000001<br>
ATOM TYPE= 5 NUM= 1 21.011011100000005<br>
22.598375300000001 12.478894200000001<br>
<br>
<br>
PROGRAM STOPS IN SUBROUTINE SETSYS| ATOMS ARE VERY CLOSE<br>
STOP 999<br>
---------------------------------------------------------------<br>
<br>
I worked only with one copper, but in the CPMD_inp.run file appears<br>
multiple copper atoms. Any suggestion about that. Thanks.<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Pradip K Biswas, PhD<br>Asst. Professor, Department of Physics,<br>Computational Bioengineering and Nanoscience Group<br>Tougaloo College, MS 39174<br>