Coarse Grain Problems

[Plácido Manuel Arenas Fernández]

Good morning,

I am starting with CG in Gromacs using Votca, is it possible to use Charmm36-forcefield instead of OPLSA? 

I have created a system of 8 asphaltenes in heptane, I have already run it in atomistic without any problem. Now I have created .xml files of heptane and Asphaltene, I have run the code

csg_map --top topol.tpr --trj confout.gro --cg "heptane.xml;a08.xml" --out conf_cg.gro  for mapping but I recieve as error: molecule 1:a08:C does not exist, I don't understand why because I have already declarated a08 in topology and everywhere. Maybe I am not doing well different steps for coarse grain, could anyone explain me?

Kind regards

Plácido

 

Plácido Manuel Arenas Fernández

Universidad Rey Juan Carlos

Campus de Móstoles  (Madrid), España

Teléfono: 91 488 85 16

placido...@urjc.es | www.urjc.es | @URJC |

 

[Christoph Junghans]

On Wed, Jul 24, 2019 at 5:26 AM Plácido Manuel Arenas Fernández <placido...@urjc.es> wrote:

Good morning,

I am starting with CG in Gromacs using Votca, is it possible to use Charmm36-forcefield instead of OPLSA? 

I have created a system of 8 asphaltenes in heptane, I have already run it in atomistic without any problem. Now I have created .xml files of heptane and Asphaltene, I have run the code

csg_map --top topol.tpr --trj confout.gro --cg "heptane.xml;a08.xml" --out conf_cg.gro  for mapping but I recieve as error: molecule 1:a08:C does not exist, I don't understand why because I have already declarated a08 in topology and everywhere. Maybe I am not doing well different steps for coarse grain, could anyone explain me?

I guess the atom is named different in the gromacs topology. 

You can run "csg_dump --top topol.tpr" to see the list of atoms VOTCA reads from the topology file.

 Christoph

Kind regards

Plácido

 

Plácido Manuel Arenas Fernández

Universidad Rey Juan Carlos

Campus de Móstoles  (Madrid), España

Teléfono: 91 488 85 16

placido...@urjc.es | www.urjc.es | @URJC |

 

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Christoph Junghans
Web: http://www.compphys.de

[Abdessamad Moumen]

Hi

I am new beginner in votca,I tray to install votca-csg several times but always i get the same error,

-- Could NOT find MKL (missing: MKL_INCLUDE_DIR MKL_Core_LINK_LIBRARY)

-- Found Eigen3: /usr/lib/cmake/eigen3

CMake Error at tools/CMakeModules/FindFFTW3.cmake:41 (message):

Could not find fftw_plan_r2r_1d in /usr/local/lib/libfftw3.a, take a look

at the error message in /home/acer/votca/build/CMakeFiles/CMakeError.log to

find out what was going wrong. If you are using a static lib (.a) make

sure you have specified all dependencies of fftw3 in FFTW3_LIBRARY by hand

(i.e. -DFFTW3_LIBRARY='/path/to/libfftw3.so;/path/to/libm.so') !

Call Stack (most recent call first):

CMakeLists.txt:78 (_find_package)

tools/CMakeLists.txt:77 (find_package)

-- Configuring incomplete, errors occurred!

See also "/home/acer/votca/build/CMakeFiles/CMakeOutput.log".

See also "/home/acer/votca/build/CmakeFiles/CmakeError.log".

could anyone explain me how to fix this problem ?

[Christoph Junghans]

What does the CMakeError.log say?

Christoph

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[Abdessamad Moumen]

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[Christoph Junghans]

My french isn't that great:
/usr/local/bin/cmake -E cmake_link_script
CMakeFiles/cmTC_6ce3b.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=fftw_plan_r2r_1d
CMakeFiles/cmTC_6ce3b.dir/CheckFunctionExists.c.o -o cmTC_6ce3b
/usr/local/lib/libfftw3.a
/usr/local/lib/libfftw3.a(mapflags.o) : Dans la fonction « fftw_mapflags » :
mapflags.c:(.text+0x3b9) : référence indéfinie vers « log »
/usr/local/lib/libfftw3.a(trig.o) : Dans la fonction « cexpl_sincos » :
trig.c:(.text+0x23c) : référence indéfinie vers « sincos »
trig.c:(.text+0x2ba) : référence indéfinie vers « sincos »
/usr/local/lib/libfftw3.a(trig.o) : Dans la fonction « fftw_mktriggen » :
trig.c:(.text+0x4c3) : référence indéfinie vers « sincos »
trig.c:(.text+0x574) : référence indéfinie vers « sincos »
trig.c:(.text+0x62b) : référence indéfinie vers « sincos »
/usr/local/lib/libfftw3.a(trig.o):trig.c:(.text+0x6e4) : encore plus
de références indéfinies suivent vers « sincos »
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_6ce3b.dir/build.make:87: recipe for target 'cmTC_6ce3b' failed
make[1]: *** [cmTC_6ce3b] Error 1

but I think you need to an fftw, which was compiled with --enable-shared.

Christoph

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