[gmx-users] pdb2gmx Could not find force field, when using -ff commandline parameter
Hello gmx-users, I wrote a script to perform a simulation on my Ubuntu 10.04 machine running Gromacs 4.0.7. At the beginning of the script I convert the system from pdb coordinates to gro using pdb2gmx. I am using the GROMOS 45a3 forcefield, specified by -ff G45a3 and it works great. pdb2gmx -f na.0.pdb -o na_initial.0.gro -ff G45a3 -water spce However, when I move the script to a Mac OS X 10.6 machine running Gromacs 4.5.4, I get the following error: Fatal error: Could not find force field 'G45a3' in current directory, install tree, or GMXDATA path The forcefield is definitely on the system and works perfectly if I don't specify the -ff argument, and instead use the interactive selection. I even copied the file to the local working directory, put it in a subdirectory named G45a3.ff (as described in the documentation) and still got the error. I also tried modifying the GMXDATA path (it was blank) to the path that contains ffG45a3.itp in /usr/share. No luck there either. Anyone have any ideas? Thanks, Keith -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
On Fri, Jan 14, 2011 at 3:58 AM, Rossen Apostolov wrote: > Hi, >> >> I get this error when I try to run mdrun-gpu with a forcefield that >> has GROMOS interaction types: >> >> Fatal error: OpenMM does not support (some) of the provided >> interaction type(s) (G96Angle). >> >> Maybe it's possible to run a short simulation on a small system and >> not encounter the missing interactions? I don't know enough about how >> the forcefields work to know whether that would get past the error. >> >> -Keith >> > > I doesn't matter whether the simulation is short or the system small. You > can exclude certain interaction types from the FF but then you'll end up > with a most likely meaningless model. > > Rossen Thank you, but I think you missed the point of my question. I was only trying to understand why Francesco might get output that is "full of NaN" instead of an error. -Keith >>> >>> Rossen >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulations on GPU
On Tue, Jan 4, 2011 at 3:17 PM, Rossen Apostolov wrote: > On 1/4/11 3:16 PM, Francesco Oteri wrote: >> >> Maybe the used force-field is wrong. >> mdrun-gpu is able to use the AMBER forcefield, but it is not possible >> using gromos force-field. >> When gromos force-field is used, the output is full of NaN > > Is that the case? > > mdrun should complain and exit if the FF isn't supported. I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing interactions? I don't know enough about how the forcefields work to know whether that would get past the error. -Keith > > Rossen > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Can't build gromacs-4.5.3 with cmake
Ah! "Outside the source tree" to me meant, outside "src/". I see now that it means outside gromacs-4.5.3. It does indeed make a difference, now I can build. When I tried to compile with OpenMM I ran into an error that I was missing libxml-2.0. I had libxml2 installed, but I needed to install the headers using: sudo apt-get install libxml2-dev. When I tried to compile I got this error: $ make mdrun [ 0%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o CMake Error at CMakeFiles/gmx_gpu_utils_generated_memtestG80_core.cu.o.cmake:256 (message): Error generating file /home/keithc/apps/gromacs-4.5.3-gpu/src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o make[3]: *** [src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 This comes from some permissions issue from when I compiled the CUDA toolkit. I had just followed directions from a post on ubuntuforums, so I think others could potentially run into this issue as well. The (inelegant) workaround was to compile as sudo: sudo make mdrun (and) sudo make install-mdrun. Now it works. Thank you! Keith -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Can't build gromacs-4.5.3 with cmake
I am running cmake version 2.8.0 on Ubuntu 10.04 64-bit with gcc 4.4.3.
~/apps/gromacs-4.5.3$ cmake -version
cmake version 2.8.0
Thanks,
Keith
>What cmake version are you using?
>
>On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg wrote:
>> Hello gmx-users,
>>
>> I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
>> have followed the INSTALL-GPU instructions along with the tips given
>> in this post:
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html
>>
>> However, I am receiving the following error from cmake even without
>> the -DGMX_OPENMM=ON flag (and I have been making sure to rm
>> CMakeCache.txt and src/CMakeCache.txt):
>>
>> user at host:~/apps/gromacs-4.5.3$ cmake src/
>> -- The C compiler identification is GNU
>> -- The CXX compiler identification is GNU
>> -- Check for working C compiler: /usr/bin/gcc
>> -- Check for working C compiler: /usr/bin/gcc -- works
>> -- Detecting C compiler ABI info
>> -- Detecting C compiler ABI info - done
>> -- Check for working CXX compiler: /usr/bin/c++
>> -- Check for working CXX compiler: /usr/bin/c++ -- works
>> -- Detecting CXX compiler ABI info
>> -- Detecting CXX compiler ABI info - done
>> -- Found assembler: /usr/bin/as
>> -- Loaded CMakeASM-ATTInformation - ASM-ATT support is still
>> experimental, please report issues
>> CMake Error at gmxlib/CMakeLists.txt:146 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at gmxlib/CMakeLists.txt:148 (install):
>> install TARGETS given no ARCHIVE DESTINATION for static library target
>> "gmx".
>>
>>
>> CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at mdlib/CMakeLists.txt:13 (install):
>> install TARGETS given no ARCHIVE DESTINATION for static library target
>> "md".
>>
>>
>> CMake Error at kernel/CMakeLists.txt:42 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at kernel/CMakeLists.txt:108 (install):
>> install TARGETS given no ARCHIVE DESTINATION for static library target
>> "gmxpreprocess".
>>
>>
>> CMake Error at kernel/CMakeLists.txt:109 (install):
>> install TARGETS given no RUNTIME DESTINATION for executable target
>> "mdrun".
>>
>>
>> CMake Error at kernel/CMakeLists.txt:110 (install):
>> install TARGETS given no RUNTIME DESTINATION for executable target
>> "grompp".
>>
>>
>> CMake Error at tools/CMakeLists.txt:36 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at tools/CMakeLists.txt:65 (install):
>> install TARGETS given no ARCHIVE DESTINATION for static library target
>> "gmxana".
>>
>>
>> CMake Error at tools/CMakeLists.txt:66 (install):
>> install TARGETS given no RUNTIME DESTINATION for executable target
>> "do_dssp".
>>
>>
>> CMake Warning (dev) in CMakeLists.txt:
>> No cmake_minimum_required command is present. A line of code such as
>>
>> cmake_minimum_required(VERSION 2.8)
>>
>> should be added at the top of the file. The version specified may be
>> lower
>> if you wish to support older CMake versions for this project. For more
>> information run "cmake --help-policy CMP".
>> This warning is for project developers. Use -Wno-dev to suppress it.
>>
>> -- Configuring incomplete, errors occurred!
>>
>> Here are my environment variables:
>>
>> PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
>>
>> LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/openmm/lib:
>>
>> The variable that seems to be empty in CMakeLists.txt is
>> ${LIB_INSTALL_DIR}. Does anyone know what that might be caused by?
>>
>> Thank you,
>> Keith Callenberg
>> --
>> gmx-users mailing listgmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>
>
>--
>ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>865-241-1537, ORNL PO BOX 2008 MS6309
--
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[gmx-users] Can't build gromacs-4.5.3 with cmake
Hello gmx-users,
I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
have followed the INSTALL-GPU instructions along with the tips given
in this post: http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html
However, I am receiving the following error from cmake even without
the -DGMX_OPENMM=ON flag (and I have been making sure to rm
CMakeCache.txt and src/CMakeCache.txt):
u...@host:~/apps/gromacs-4.5.3$ cmake src/
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found assembler: /usr/bin/as
-- Loaded CMakeASM-ATTInformation - ASM-ATT support is still
experimental, please report issues
CMake Error at gmxlib/CMakeLists.txt:146 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at gmxlib/CMakeLists.txt:148 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
"gmx".
CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at mdlib/CMakeLists.txt:13 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
"md".
CMake Error at kernel/CMakeLists.txt:42 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at kernel/CMakeLists.txt:108 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
"gmxpreprocess".
CMake Error at kernel/CMakeLists.txt:109 (install):
install TARGETS given no RUNTIME DESTINATION for executable target "mdrun".
CMake Error at kernel/CMakeLists.txt:110 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
"grompp".
CMake Error at tools/CMakeLists.txt:36 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at tools/CMakeLists.txt:65 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
"gmxana".
CMake Error at tools/CMakeLists.txt:66 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
"do_dssp".
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 2.8)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring incomplete, errors occurred!
Here are my environment variables:
PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/openmm/lib:
The variable that seems to be empty in CMakeLists.txt is
${LIB_INSTALL_DIR}. Does anyone know what that might be caused by?
Thank you,
Keith Callenberg
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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