[gmx-users] Re: removing rotational and translational motion (holonomic contraint)
deplazes
e.deplazes at uq.edu.au
Mon Mar 18 06:12:15 CET 2013
Hi Tsjerk
thanks for the patch. I have a few problems and questions
1. I get an error message when installing the patch version. This is what I
did
tar -xvf gromacs-3.3.1-rtc.tar
module load intel/12.1
module load intel-mkl/10.3.9
module load fftw/3.3.3
module load openmpi/1.6.3
export LDFLAGS="-L/ivec/devel/intel/12.1/fftw/3.3.3/lib"
export CPPFLAGS="-I/ivec/devel/intel/12.1/fftw/3.3.3/include"
cd /home/deplazes/gromacs-3.3.1-rtc
./configure --prefix=/home/deplazes/gromacs-3.3.1-rtc --with-fft=fftw3
make -j4
make install
I get an error message when running make -j4, see below at the end of this
post. I used the same commands to install gromacs 3.3.3 and 3.3.1 (normal
version) and had no issues.
It looks like a error in /src/tools/gmx_metric.c
(If I add the semi-colon on line 50 after the typedef I simply get other
errors)
After I have installed the "patched" version
2. to"switch on" the roto-translational constraints I set
rototr = yes
in the .mdp file, correct?
according to a previous post I also need a reference structure (
ref_conf.gro). do I need to add this as an option during grompp? if so, what
command option / flag do I use? if not during grompp how do I add the
reference structure?
3. the two examples in the paper are for a NVT and a NVE ensemble. is it ok
to use the restraints for an NPT run? I have not found any reference to it
in the paper.
thanks
Evelyne
-------------------------------------------------------------------------------
error from "make -j4"
gmx_metric.c(50): error: expected a ";"
void init_matblock( int i, int j, matblock *A )
^
gmx_metric.c(133): error: expected a declaration
}
^
gmx_metric.c(136): error: expected a declaration
}
^
gmx_metric.c(173): error: declaration is incompatible with "char
*index(const char *, int)" (declared at line 489 of "/usr/include/string.h")
atom_id *index;
^
gmx_metric.c(175): error: expected a ")"
CopyRight(stderr,argv[0]);
^
gmx_metric.c(176): error: expected a type specifier
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
^
gmx_metric.c(176): error: identifier "argv" is undefined
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
^
gmx_metric.c(176): error: expected a type specifier
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
^
gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: identifier "fnm" is undefined
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: identifier "pargs" is undefined
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: identifier "desc" is undefined
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(177): error: expected a type specifier
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
^
gmx_metric.c(179): error: function "ftp2fn" is not a type name
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected a ")"
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected a type specifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: identifier "fnm" is undefined
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: declaration is incompatible with "char *title"
(declared at line 166)
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected an identifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected an identifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected an identifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected a ")"
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: declaration is incompatible with "matrix box"
(declared at line 169)
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(179): error: expected an identifier
read_tps_conf( ftp2fn(efTPS,NFILE,fnm), title, &top, &xref, NULL, box,
TRUE);
^
gmx_metric.c(180): error: declaration is incompatible with "real={float}
*w_rls" (declared at line 170)
snew(w_rls,top.atoms.nr);
^
gmx_metric.c(180): error: variable "w_rls" has already been initialized
snew(w_rls,top.atoms.nr);
^
gmx_metric.c(180): error: function call is not allowed in a constant
expression
snew(w_rls,top.atoms.nr);
^
gmx_metric.c(180): error: operand of "*" must be a pointer
snew(w_rls,top.atoms.nr);
^
gmx_metric.c(180): error: expression must have a constant value
snew(w_rls,top.atoms.nr);
^
gmx_metric.c(182): error: expected an identifier
fprintf(stderr,"Select group for distance calculation\n");
^
gmx_metric.c(183): error: expected a type specifier
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: function "ftp2fn_null" is not a type name
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: expected a ")"
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: expected a type specifier
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: identifier "fnm" is undefined
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: expected an identifier
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: expected an identifier
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: expected an identifier
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(183): error: expected an identifier
get_index( &top.atoms, ftp2fn_null(efNDX,NFILE,fnm), 1, &n, &index,
&grpnames);
^
gmx_metric.c(186): error: expected a declaration
for( i=0; i<n; i++ )
^
gmx_metric.c(189): error: expected a declaration
if (bFit)
^
gmx_metric.c(193): error: function call is not allowed in a constant
expression
nfiles1 = opt2fns(&fnms1,"-f",NFILE,fnm);
^
gmx_metric.c(193): error: identifier "fnm" is undefined
nfiles1 = opt2fns(&fnms1,"-f",NFILE,fnm);
^
gmx_metric.c(194): error: expected a declaration
if (!nfiles1)
^
gmx_metric.c(197): error: function call is not allowed in a constant
expression
nfiles2 = opt2fns(&fnms2,"-f2",NFILE,fnm);
^
gmx_metric.c(199): error: expected a declaration
for ( i=0; i<nfiles1; i++ )
^
gmx_metric.c(202): error: expected a declaration
for ( i=0; i<nfiles2; i++ )
^
gmx_metric.c(205): error: expected a type specifier
exit(0);
^
gmx_metric.c(209): error: expected a declaration
}
^
make[3]: *** [gmx_metric.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory `/home/deplazes/gromacs-3.3.1-rtc/src/tools'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/deplazes/gromacs-3.3.1-rtc/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/deplazes/gromacs-3.3.1-rtc/src'
make: *** [all-recursive] Error 1
--
View this message in context: http://gromacs.5086.n6.nabble.com/removing-rotational-and-translational-motion-holonomic-contraint-tp5006265p5006396.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
More information about the gromacs.org_gmx-users
mailing list