Re: [gmx-users] generating movie file

[Alex]

No, there are other tools for that (e.g. pymol + avidemux).

I too was wondering if trjconv could produce an mp4 and add Morgan 
Freeman's voice as narration to my glorious trajectory, but was 
disappointed. Very useful for supplemental files for journals with 
IF>10. Maybe gmx developers should look into that.



On 1/26/2018 9:51 PM, Vidya R wrote:

Hi gromacs users,


Can we generate .mp4 file instead of .pdb using gmx trjconv?

Thanks,
Vidya.R


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[gmx-users] generating movie file

[Vidya R]

Hi gromacs users,


Can we generate .mp4 file instead of .pdb using gmx trjconv?

Thanks,
Vidya.R
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[gmx-users] Using libgromacs in a CMake project built on the fly?

[Cory J. Geesaman]

Is it possible to use libgromacs in a CMake based project which links the
library in at build time (but from source as opposed to a system-wide
installation?)

 

So far I have the gromacs source included as a submodule from
https://github.com/gromacs/gromacs.git located in the subdirectory
3rdparty/gromacs/

 

In my CMakeLists.txt I have:

 

include_directories(${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/gromacs/src/gromacs
)

 

and a bit further down:

 

target_link_libraries(${PROJECT_NAME} ${Boost_LIBRARIES} libgromacs)

 

Which seems to pass the CMake tests, but when it gets to actually building
the project I get the error:

 

c:/progra~1/mingw/bin/../lib/gcc/x86_64-w64-mingw32/7.2.0/../../../../x86_64
-w64-mingw32/bin/ld.exe: cannot find -llibgromacs

collect2.exe: error: ld returned 1 exit status

 

I'm sure this is some kind of CMake error but I don't know what it could be
precisely because I'm relatively new to CMake.  I'm building with
CLion+MinGW on Windows 7 (but also intend to build on Linux.)

 

Additionally, are there any significant gromacs-specific performance
concerns I should be aware of building Windows binaries with MinGW or will
it work as well as with a Windows build platform like visual c++?

 

Thanks for any information,

Cory

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[gmx-users] Compiling Gromacs 2018 using Intel 2018.1 compiler on OSX 10.13.3

[Zhiyi Wu]

Hi,
I’m trying to compile Gromacs 2018 with icc 2018.1.126 on a iMac using flag

cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_GPU=on 
-DGMX_USE_OPENCL=on -DGMX_SIMD=AVX2_256 -DGMX_FFT_LIBRARY=mkl 
-DREGRESSIONTEST_DOWNLOAD=ON

The cmake succeed without any warning but during the making I have encountered 
an error.

[ 23%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o
/Users/zhiyiwu/src/gromacs-2018/src/gromacs/gmxana/gmx_dipoles.cpp(257): error: 
expected an identifier
  if (debug || std::isnan(cosa))
compilation aborted for 
/Users/zhiyiwu/src/gromacs-2018/src/gromacs/gmxana/gmx_dipoles.cpp (code 2)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o] 
Error 2
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

I have repeated the same compilation on another Mac and encountered the same 
error. I have tried to replace icc with GCC7 and the compilation succeed 
without any error. I have also tried to compile the same Gromacs on a Linux 
with the same 2018.1 intel compiler (2018.1.163) and it succeeded without any 
error.
It seems that this error only occurred when using icc on a Mac. I wonder if 
there is any way of solving this problem? Thanks,
Kind regards,
Zhiyi Wu
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Re: [gmx-users] How to convert charmm str to itp file?

[Justin Lemkul]

On 1/25/18 10:53 PM, 金 瑞涛 wrote:

Greetings Miji

That means you need to install netwokx.
Try pip install networkx. if you still get other problem, it might caused by 
the lasted networkx, try the old version if other problem occurs, unless you 
are still missing other module.


Just as a bit of clarification - networkx version 2.x is incompatible 
with our script, but anything in the 1.x series works fine.


-Justin

--
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Virginia Tech Department of Biochemistry

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==

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Re: [gmx-users] Output velocities and forces for each step?

[Mohd Farid Ismail]

Is there a way to split the coordinates, velocities, and forces into separate .trr files? -- Mohd Farid Ismail26.01.2018, 15:00, "Mohd Farid Ismail" :That does it. Thank you for your quick reply. -- Mohd Farid Ismail26.01.2018, 13:19, "Shrinath Kumar" :1. No, they are written at whatever frequency you specify in your mdp file.Look at the nstxout, nstvout and nstfout options. You can choose to writethem to the .trr file at each step if you wish.3. You can use gmx traj -ov -ofOn 26 January 2018 at 04:55, Mohd Farid Ismail 

[gmx-users] printf + trjcat

[Hector Martinez-Lopez]

Hey! I'm trying to use


```

printf "c\nc\nc" | trjcat -f 1.trr 2.trr 3.trr -o all.trr -settime

```


without results. I readed in other threads, here at the list, that it can be 
used as:


```

trjcat -f 1.trr 2.trr 3.trr -o all.trr -settime  | T. +34 934020938 - +45 
39178231

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Mind the Byte SL | Barcelona Science Park | C/ Baldiri Reixac, 4-8 | 08028

Mind the Byte ApS | Copenhagen Bio Science Park | Ole Maaløes Vej 3 | DK-2200 
Copenhagen N


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@mindthebyte
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