[gmx-users] Reordering of water molecules with Na+ ions coordinates in xtc message

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jan 1 17:58:41 CET 2011

Dear Leila:

I looked at the source file that you sent me by personal email looks correct.

Did you use the correct version of the template directory? My makefile  
looks like this (see below). If you used I am not sure where you gt  
the makefile since you mentioned many different places in your online  
posts and by email, but be sure that you are using the one produced by  
the 4.0.7 compilation.


# Generated automatically from Makefile.in by configure.
# This is a Gromacs 3.0 my_tool makefile for your own utility programs.
# Copy this file to whatever directory you are using for your own
# software and add more targets like the my_tool one below.
# If you are using gmake it is relatively straightforward to add
# an include based on environment variables (like previous Gromacs versions)
# to select compiler flags and stuff automatically, but below it is static:

# Variables set by the configuration script:
LIBS         = -lmd -lgmx -lnsl -lfftw3f -lm
LDFLAGS      =  
CFLAGS       = -O3 -fomit-frame-pointer -finline-functions -Wall  
-Wno-unused -funroll-all-loops   
CC           = cc
LD           = $(CC)

# The real make targets - note that most make programs support
# the shortcut $^ instead of listing all object files a second
# time, but we cannot count on it...

my_tool:        my_tool.o
                 $(LD) $(LDFLAGS) -o $@ my_tool.o $(LIBS)

I found gmx_trjconv.c file, It is in gromacs-4.0.7/src/tools.
since location of template directory is as follows:
I used cp gmx_trjconv.c ../../share/template/my_tool.c.
is it true?
I did those changes you said in my_tool.c file.
I created makefile without problem using sed "s/template/my_tool/g"
Makefile.x86_64-unknown-linux-gnu > Makefile.my_tool.
but when compile it, I encountered with following errors:

cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops   -I/usr/include/libxml2 -I/usr/local/gromacs/include
-I/usr/local/gromacs/include/gromacs     -c -o my_tool.o my_tool.c
my_tool.c: In function ?calc_pbc_cluster?:
my_tool.c:88: error: ?bool? undeclared (first use in this function)

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