hits-mbm / gromacs-fda Goto Github PK

Im currently trying to investigate my protein using the latest gmx_fda version but struggle with fda_graph.
Running gmx_fda mdrun -nt 1 -rerun system.cat.xtc -s ../../topol.tpr -pfn index.ndx -pfi input.pfi works fine. But echo Protein | gmx_fda fda_graph -i fda.pfr -s ../../topol.tpr -n index.ndx fails with

Fatal error:
Number of atoms in group 21792 does not match number of FDA points 37812.

(Protein group has 21792 elements)
37812 corresponds to the total number of residues in my system, including ions and water.
From the manual i concluded that only residues in the Protein group should have been considered, i also included energy_grp_exclusion = yes in my input file but that didn't changed the number of FDA points.

Question is: How to construct a proper index file for fda_graph?

input.pfi:

onepair = summed
group1 = Protein
group2 = Protein
type = all
atombased = no
residuebased = pairwise_forces_scalar

Annual merge to the next major version.

Hi Bernd,

I am trying to install FDATools to directly import and analyze my average pair-wise force data (.fm file) using atomGraph and resGraph within the package. On typing <install.packages('FDAtools')> on R console, I am receiving the following error :
Warning in install.packages
package ‘FDAtools’ is not available (for R version 3.3.3)

Which version of R has FDAtools package? Looking forward to hearing from you.

Thanks,
Khushboo

I have output .xtc files for my simulations and I get an error saying their are no velocities. Do I have to run the simulation again writing out velocities or will the FDA work regardless of the error?

Thanks,
Daniel

When we get to the make install of the FDA patch we get an error:

-- Up-to-date: /N/u/dbiner/BigRed2/software/gromacs/fda-08232016/include/gromacs/trajectoryanalysis/analysismodule.h
-- Up-to-date: /N/u/dbiner/BigRed2/software/gromacs/fda-08232016/include/gromacs/trajectoryanalysis/analysissettings.h
-- Up-to-date: /N/u/dbiner/BigRed2/software/gromacs/fda-08232016/include/gromacs/trajectoryanalysis/cmdlinerunner.h
CMake Error at src/programs/cmake_install.cmake:42 (file):
file INSTALL cannot find
"/N/u/dbiner/BigRed2/software/gromacs/fda-08232016/bin/gmx".
Call Stack (most recent call first):
src/cmake_install.cmake:40 (include)
cmake_install.cmake:48 (include)

make: *** [install] Error 1

Any suggestions?

Also, is the FDA patch supposed to be installed in the GROMACS install directory?

Thanks for all your help!

Dan

Error during compilation:

In file included from /home/doserbd/git/gromacs-fda/src/gromacs/gmxana/gmx_fda_shortest_path.cpp:9:0:
/home/doserbd/git/gromacs-fda/src/gromacs/gmxana/fda/BoostGraph.h:11:42: fatal error: boost/graph/adjacency_list.hpp: No such file or directory
 #include <boost/graph/adjacency_list.hpp>

The error is from gromacs v2016.

Hello,

the documentation of the vector2scalar option "norm" states that,

if it's positive, the vector force is oriented within -90 to 90 degrees with respect to the atoms/residues - considered to be same direction = attractive = negative
if it's negative, the vector force is oriented within 90 to 270 degrees with respect to the atoms/residues - considered to be in opposite direction = repulsive = positive

This is rather ambiguous! What exactly does "positive [...] = negative" and "negative [...] = positive" mean? Which is the correct sign? Should it maybe say "if the cosine is positive/negative, the vector force is ..." and "= attractive/repulsive = the assigned sign is negative/positive"?

Thank you!
Best,
Ferdinand

FILE_OUT_NONE is not treated at

#23 wasn't a bug and was caused by a misunderstanding of the fact that pdb coordinates are in angstrom whereas gro coordinates are in nm. Therefore, I will reverse the commits cc8b30a and 0a894f4.

I'm trying to use the fda_shortest_path module for the analysis with the following comand

gmx_fda fda_shortest_path -i output.pfr -s md.tpr -n index.ndx -o shortest.pdb

and I receive the following error message:

Fatal error:
Error opening file fda.pfa

If you notice from my input file, I performed the analysis residue-based and not atom-based, thus I only have an output.pfr file and not a out.pfa.
As a test, I created an empity fda.pfa file and the analysis work without printing anything in the output.
I suppose this could be due to a problem in the code because it seems the algo requires a specific file called fda.pfa

FDA will be added to Verlet non-bonded SIMD kernels, similar to the existing Verlet reference kernel.

Hello,

I've installed fda on my school's hpc and am getting the following error:

Program: gmx mdrun, version 2020.4-dev-20220124-df2cd772a-unknown

Standard library runtime error (possible bug):
(exception type: St13runtime_error)
Unknown option yes

Perhaps I didn't have some module/dependency loaded when I installed?

I am also trying to install locally on an M1 mac but getting a list of errors there.

Thank you,

Dan

At the moment invalid options will be ignored. e.g. if the deprecated option 'scalar' is used instead of the 'pairwise_forces_scalar' and there will be no result file.

In the manual https://github.com/HITS-MBM/gromacs-fda/blob/release-2020-fda/fda-manual/fda-manual.pdf I noticed some typing mistakes. Keep in mind I am not a native speaker and not an expert in the field. I could not compile a patch, because I could not find the source of the file. Hence, I created this issue.

At first you see the current spelling. Then a separator line. At the end of the separator line you might see "multi". This indicates that this particular item can be found multiple times in the document. After the separator line you see my suggested fix.

the gromacs version
--
the GROMACS version


numbers ar identical
--
numbers are identical


  -b <gromacs-version>-fda<fda-version>
--
  -b release-<version, usually year>-fda


1. building of an atom to residue correspondence table
--
1. building of an atom according to residue correspondence table


f.e.
-- multi
f.i.


F.e.
--
F.i.


contiguous
-- multi
continuous


representations !
--
representations!


forcefield
--
force field


indeces
-- multi
indices (or indexes)

The fda_graph option 'big' produce the same results (all networks) with or without the flag.

To be consistent to the other analysis modules of gromacs the optional flag '-traj' will be changed into '-f' for the FDA analysis modules fda_graph, fda_shortest_path, and fda_view_stress.

Hi @BerndDoser

I've used gmx_fda V 2.10 for GROMACS 2020.1 to generate a PFR file using the following command:

gmx_fda mdrun -nt 1 -rerun r1pr_3fcs_2d_skip10.xtc -pfi input.pfi -pfr out_test.pfr -s r1pr_3fcs_2d.tpr -pfn index.ndx

Where the input.pfi file contains the following parameters:

onepair = summed
group1 = Protein
group2 = Protein
residuebased = pairwise_forces_scalar
type = all
time_averages_period = 10

This outputs the expected PFR file, and it resembles those provided in your gromacs-fda-vmd repository alagly examples. However, I can't visualise this output; I've tried the VMD scripts, following the examples on pages 16 and 17 of the FDA manual, and using fda_graph to convert the PFR file to a pymol file or a PDB.

The former looks like it works throughout (i.e. the TCL console prints out "now loading inter-residue pairwise forces" and a pf_minmax value) but neither the pf_draw or trace variable vmd_frame(0) w pf_draw commands appear to output the expected cylinders. I can get the correct output for the residue-based alagly example from the previously mentioned repository, with the cylinders.

Also, when I try and run:
gmx_fda fda_graph -i out_test.pfr -s r1pr_3fcs_2d.tpr -f r1pr_3fcs_2d_skip10.xtc -n index.ndx -o fda_graph_output_test.pdb -pymol fda_graph_output_test_pymol_traj.pml

I get an error that the "Number of atoms in group 292 does not match the number of FDA points 294". From my NDX file, I know that the protein is comprised of 292 C-alpha's, so I assume that the cause of the mis-numbering is due to residue renumbering by gmx_fda? If true, unfortunately when I turn off residue renumbering, I get a SegFault 11 immediately after the notification that "Residue number collision detected, residues will NOT be renumbered", so I can't test this.

Any help would be greatly appreciated; I'm happy to send you any of the input and output files privately if that helps.

Hi Bernd,

I'm a little confused about the VMD visualization plugins. Is this the website to download the latest version of pf2 VMD plugins?
https://github.com/HITS-MBM/fda-archive

When using
vmd-plugins_pf2_20120829.tar.gz
and importing

package require pf_loaduser
pf_loaduser <filename.pfr>

in VMD, I got the following error,
expected floating-point number but got "pairwise_forces_scalar".
Seems it could not read the phrases like
"pairwise_forces_scalar
frame 0"
from my .pfr file. Only when I delete these lines manually, it can work.
Is this normal or I did something wrong?
Thanks!

Wen

Hi, Bernd!

I conducted (TR)FD analysis to investigate the effect of a mutation on the force propagation within a protein-ligand complex. Now, I need to generate images for my publication highlighting the difference in the force distribution from the point of mutation between wild-type and mutant protein. I was hoping to generate a network representation of the force distribution within the protein, a figure similar to the one attached, Fig 2 (C). My figure looks very different (attached); the image was generated using .pfa and pf_draw package within VMD 1.9.1 as suggested in the manual.

It would be of great help if you could advise me on how to obtain network representation of force distribution from a particular residue.

The leading signs of the pairwise forces are calculated with the directions of the force and the bond vectors (see

Dear fda developers,
I am trying to use gromacs-fda to calculate punctual stress during the course of a steered MD simulation.
My input file looks like this

onepair = summed
atombased = no
residuebased = punctual_stress
type = all

gmx_fda mdrun completes without any error and the output .psr files are written.
However, when I try to generate PDB files using
gmx_fda fda_view_stress -i output1.psr -s ../structure.tpr -f ../traj.xtc -n ../index.ndx -o stress1.pdb -frame 1 -convert yes
I get segmentation fault.
When it asks for residue model points, I have tried Protein and C-alpha but none works.
The final output looks like this

stress filename = output1.psr
result filename = stress1.pdb
frameType = single
frameValue = 1
stressType = punctual
particleType = residue
convert = 1
Reading file ../WT-100pN-500ns-1.tpr, VERSION 2020.4 (single precision)
Reading file ../WT-100pN-500ns-1.tpr, VERSION 2020.4 (single precision)

Back Off! I just backed up stress1.pdb to ./#stress1.pdb.3#
Segmentation fault (core dumped)

I would really appreciate any help/suggestions.

Best,
Amin.
Center de Biochimie Structurale,
Montpellier,
France.

All frame numbers are zero.

Hello,

I previously asked a question here you regarding running Gromacs-FDA for a coarse-grained model. I successfully ran Gromacs-FDA with my files but now I have a question about getting .psa files for coulombic interactions. When I choose coulomb as the interaction type, I get 0 for all the values in the .psa file. I don't have this issue with other interaction types.
Can you please help me with this?

Thanks,
Mohaddeseh

A new option "normalize_punctual_stress_per_residue" will be added to FDA, which divide the per-residue punctual stress by the number of atoms in the residue.

Issue can be reproduced using the alagly test system at src/gromacs/gmxana/fda/tests/data/alagly with

gmx_fda fda_graph -i fda.pfr -s conf.gro -t 1000 -n index.ndx

result.pdb:

ATOM      1              2      -0.410  -1.740  -1.310  1.003437.44      AA
ATOM      2              3      -0.410  -1.740   0.330  1.003437.44      AA
CONECT    1    2
ENDMDL

shows wrong coordinates.

The stress values printed in the B-factor column of the PDB file using the FDA analysis too fda_view_stress are wrong. All frames are identical and showing a single trajectory state.

I used gmx_fda mdrun to calculate pairwise forces between atoms (saved to out.pfa). Now I am trying to use fda_get_stress to calculate the punctual stress per atom from the pairwise forces.

When I run it with the following command: gmx_fda fda_get_stress -i out.pfa -o stress.psa, it seems like the function ignores the file given with option -i and falls back to the default. I get this error. Fatal error: Error opening file fda.pfa

When I put a file fda.pfa in my current directory, it runs as I would expect, with the output:

pfx filename = out.pfa
result filename = stress.psa
nbFrames = 1
nbParticles = 22
All done.

Curiously, it also works if I provide a second file with -diff.

I am running the (currently latest) release v2020.4-fda2.10.2.

Using a large index group (ndx-file) with indices larger than 1.000.000 the fda rerun aborts with:

ResidueRenumber: yes
Vector2Scalar: norm
Pairwise interactions selected: all
Pairwise forces for groups: Protein and Protein
Residues will be renumbered.
Binary mode: 0
Threshold: 1e-10
Normalize punctual stress per residue: 0
Ignore missing potentials: 0
double free or corruption (out)

Conversion from nm into angstrom is not considered:

Hello,

We tried to install gromacs-fda on ubunto but got the following errors after executing the 'make' command:
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp: In function ‘int gmx_fda_view_stress(int, char**)’:
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:128: warning: ‘auto’ will change meaning in C++0x; please remove it
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:128: error: expected initializer before ‘:’ token
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:131: error: expected primary-expression before ‘if’
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:131: error: expected ‘;’ before ‘if’
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:131: error: expected primary-expression before ‘if’
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:131: error: expected ‘)’ before ‘if’
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:131: warning: ‘auto’ will change meaning in C++0x; please remove it
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:131: error: expected initializer before ‘:’ token
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:133: error: expected primary-expression before ‘title’
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:133: error: expected ‘;’ before ‘title’
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:133: error: ‘title’ was not declared in this scope
/home/mohammad/Downloads/gromacs-fda-fda/src/gromacs/gmxana/gmx_fda_view_stress.cpp:133: error: expected ‘)’ before ‘;’ token

Could you please help me resolve this issue?

Thanks,
Hengameh

Most likely the intention of the check was to ensure that all residue interactions are covered, which makes only somehow sense for complete protein self-interactions. For interactions between two proteins the check will fail.

The line will be removed in the analysis modules fda_graph, fda_shortest_path, and fda_show_stress.

Hi Bernd,

I am trying to install the v2016.1-fda2.7 in a new macbook, after following the fda manual , terminal was showing as follow:

cmake -DCMAKE_INSTALL_PREFIX=/Users/cs/gromacs/fda-2016.1-fda2.8 -DGMX_BUILD_FDA=ON -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_fda -DGMX_SIMD=NONE -DGMX_BUILD_UNITTESTS=ON -DGMX_GPU=OFF ..

-- The C compiler identification is AppleClang 8.1.0.8020042
-- The CXX compiler identification is AppleClang 8.1.0.8020042
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Try OpenMP C flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
CMake Warning at cmake/gmxManageOpenMP.cmake:70 (message):
The compiler you are using does not support OpenMP parallelism. This might
hurt your performance a lot, in particular with GPUs. Try using a more
recent version, or a different compiler. For now, we are proceeding by
turning off OpenMP.
Call Stack (most recent call first):
CMakeLists.txt:319 (include)

-- Performing Test CFLAGS_PRAGMA
-- Performing Test CFLAGS_PRAGMA - Success
-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_WARN_EXTRA
-- Performing Test CFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_PRAGMA
-- Performing Test CXXFLAGS_PRAGMA - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_WARN_EXTRA
-- Performing Test CXXFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_DEPRECATED
-- Performing Test CXXFLAGS_DEPRECATED - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - not found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - not found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Failed
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - not found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - found
-- Checking for mm_malloc()
-- Checking for mm_malloc() - supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- graph
-- Looking for zlibVersion in /usr/lib/libz.dylib
-- Looking for zlibVersion in /usr/lib/libz.dylib - found
-- Could NOT find Hwloc (missing: HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS) (Required is at least version "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test callconv___vectorcall
-- Performing Test callconv___vectorcall - Success
-- Checking for module 'fftw3f'
-- Found fftw3f, version 3.3.6-pl2
-- Looking for fftwf_plan_r2r_1d in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib
-- Looking for fftwf_plan_r2r_1d in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib - found
-- Looking for fftwf_have_simd_sse in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib
-- Looking for fftwf_have_simd_sse in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib - not found
-- Looking for fftwf_have_sse in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib
-- Looking for fftwf_have_sse in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib - not found
-- Looking for fftwf_have_simd_sse2 in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib
-- Looking for fftwf_have_simd_sse2 in /usr/local/Cellar/fftw/3.3.6-pl2/lib/libfftw3f.dylib - found
objdump: Unknown command line argument '--reloc'. Try: '/Library/Developer/CommandLineTools/usr/bin/objdump -help'
objdump: Did you mean '-color'?
-- Using external FFT library - FFTW3
-- Looking for dgemm
-- Looking for dgemm - found
-- A library with BLAS API found.
-- Looking for cheev
-- Looking for cheev - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using manually set binary suffix: "_fda"
-- Using manually set library suffix: ""
-- Found PythonInterp: /usr/local/bin/python2.7 (found suitable version "2.7.13", minimum required is "2.7")
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/cs/gromacs-fda-2016.1-fda2.8/build

and after typing make, it was showing error as follow

[ 32%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fda/Graph.cpp.o
[ 32%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fda/Helpers.cpp.o
[ 32%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fda/Node.cpp.o
[ 32%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fda/PDB.cpp.o
/Users/cs/gromacs-fda-2016.1-fda2.7.1/src/gromacs/gmxana/fda/PDB.cpp:79:12: error: use of undeclared identifier 'sqrt'
int dim = sqrt(forceMatrix.size());
^
1 error generated.
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fda/PDB.cpp.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Is there anything wrong with my gcc version? And do you know how to fix the compiling error?
Thank you

For all FDA result files (pfa, pfr, psa, psr, vsa, vma) a binary format will be implemented for the FDA rerun and the FDA trajectory analysis tools.

This issue is related to #34. If a residue FDA point have no force interaction it was throwing a fatal error "Error in insertPDBInfo".

The exit will be changed into a loop continue.

cmake works fine, but make fails with the following error:

/Users/mohammad/Downloads/gromacs-fda-2019.3-fda2.9.1/src/gromacs/mdlib/shake.cpp:228:10: error: no member named 'qsort' in namespace 'std' std::qsort(sb, ncons, sizeof(*sb), pcomp);
1 error generated.
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Commenting out the qsort line results in a successful compile but gives error at linking stage.

FDA version: 2019.3
OS: macOS High Sierra 10.13.6
Compiler: clang

• Remove duplicated structures t_pf_global_data and t_pf_global
• Move documentation from impl into header files
• Use C++ classes instead of structures and free functions

I can reproduce the issue within a fedora docker container:

FROM fedora:31

LABEL maintainer="Bernd Doser <[email protected]>"

RUN yum install -y cmake boost-devel wget make gcc-c++
RUN wget https://github.com/HITS-MBM/gromacs-fda/archive/v2019.3-fda2.9.1.tar.gz
RUN tar xvf v2019.3-fda2.9.1.tar.gz
RUN mkdir gromacs-fda-2019.3-fda2.9.1/build
WORKDIR gromacs-fda-2019.3-fda2.9.1/build
RUN cmake -DGMX_BUILD_MDRUN_ONLY=OFF -DGMX_BUILD_FDA=ON -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_fda -DGMX_SIMD=NONE -DGMX_BUILD_UNITTESTS=ON -DGMX_BUILD_OWN_FFTW=ON -DBoost_DEBUG=1 ..

It looks like the FindBoost module of CMake is not working with the fedora boost installation. Library (/usr/lib64/libboost_graph.so) and header files (/usr/include/boost/graph) are available but not found by FindBoost.cmake.

Originally posted by @BerndDoser in #6 (comment)

For the storage of the pairwise forces the wrong atom indices are used for the CMAP bond type.

Some bond potentials (low_angres, restrangles, restrdihs, cbtdihs, and cmap_dihs) are not supported by FDA and stop with an error message. A new FDA option ‘ignore_missing_potentials’ will be added to print only a warning. Be aware that the sum of distributed forces do not agree with the total forces. The default value is false.

Hi,

I am trying to rerun my trajectory to recompute the atomic forces using (TR)FDA. After running for a while, my job stops due to an error (pasted below). I am not sure if this is related, but while generating my tpr file, I did not get any LINC warnings. It would be of great help if you could guide me as to what could lead to such error.

Program mdrun_pf2, VERSION 4.5.3
Source code file: constr.c, line: 176
Fatal error:
Too many LINCS warnings (1009)
If you know what you are doing you can adjust the lincs warning threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Thanks,
Khushboo Singh
Ph.D. Candidate

Hi,
I was wondering if it is possible to use FDA for a one-bead-per-amino-acid coarse-grained molecular dynamics model that runs on Gromacs. I have tried to run it but I get empty output files. In the model that I use, only residues are taken into account and the interactions are defined between residues, so I have no atomic information in the input files that I use for FDA.
Thanks in advance,
Mohaddeseh