[gmx-users] Strange in PMF calculation
Shi Li
sli259 at g.uky.edu
Thu Nov 24 00:44:02 CET 2016
>>>
>>> ________________________________________
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
>>> Abraham <mark.j.abraham at gmail.com>
>>> Sent: 23 November 2016 15:33:09
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] Unable to compile plug-in support for gromacs
>>> 5.1.2
>>>
>>> Hi,
>>>
>>> Offhand the first error is inexplicable, but the first is that the linker
>>> flags aren't set up right. However I do think we fixed that at some
>>> stage...
>>>
>>> Mark
>>>
>>> On Wed, 23 Nov 2016 21:23 Christopher Neale <
>> chris.neale at alum.utoronto.ca>
>>> wrote:
>>>
>>>> I've now also tried gromacs 4.6.7 and though I was not able to compile
>>>> with plugin support, I did get more error messages there.
>>>>
>>>> Compiling gromacs 4.6.7 in the same way, I still see this output during
>>>> compilation:
>>>>
>>>> -- Checking for dlopen
>>>> -- Performing Test HAVE_DLOPEN
>>>> -- Performing Test HAVE_DLOPEN - Success
>>>> -- Checking for dlopen - found
>>>>
>>>> However, in gmx4.6.7 (but not 5.1.2) compilation, I get the errors:
>>>>
>>>> [ 55%] Building C object
>>>> share/template/CMakeFiles/template.dir/template.c.o
>>>> [ 55%] Linking C executable template
>>>> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlopen':
>>>> vmddlopen.c:(.text+0x6): undefined reference to `dlopen'
>>>> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlerror':
>>>> vmddlopen.c:(.text+0x11): undefined reference to `dlerror'
>>>> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlsym':
>>>> vmddlopen.c:(.text+0x21): undefined reference to `dlsym'
>>>> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlclose':
>>>> vmddlopen.c:(.text+0x31): undefined reference to `dlclose'
>>>> collect2: ld returned 1 exit status
>>>> make[2]: *** [share/template/template] Error 1
>>>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>>>> make[1]: *** Waiting for unfinished jobs....
>>>>
>>>>
>>>> ### But I do have dlfcn.h in a standard location that should get picked
>>> up
>>>> by an #include statement:
>>>>
>>>> $ ls /usr/include/dlfcn.h
>>>> /usr/include/dlfcn.h
>>>>
>>>> Still, I tried exporting CMAKE_INCLUDE_PATH=/usr/include and compiled
>>>> again (clean build directory) but got the same problem (and same thing
>>> if I
>>>> used -DCMAKE_INCLUDE_PATH=/usr/include as a cmake argument).
>>>>
>>>> Thanks again for any help,
>>>> Chris.
>>>> ________________________________________
>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
>>>> Christopher Neale <chris.neale at alum.utoronto.ca>
>>>> Sent: 23 November 2016 13:23:52
>>>> To: Discussion list for GROMACS users
>>>> Subject: [gmx-users] Unable to compile plug-in support for gromacs
>> 5.1.2
>>>>
>>>> This sender failed our fraud detection checks and may not be who they
>>>> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>>>>
>>>> Dear Users:
>>>>
>>>> I tried to compile gromacs 5.1.2 with plugin support, but upon running
>>> gmx
>>>> trjconv I get the following error message indicating that plugin
>> support
>>>> was not actually included:
>>>>
>>>> $ /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial_plugins/bin/gmx
>>>> trjconv -f MD1.mdcrd.nc -s EM.gro -o a.xtc
>>>>
>>>> <... snip ...>
>>>>
>>>> Fatal error:
>>>> Not supported in read_first_frame: MD1.mdcrd.nc. Please make sure that
>>>> the file is a trajectory.
>>>> GROMACS is not compiled with plug-in support. Thus it cannot read
>>>> non-GROMACS trajectory formats using the VMD plug-ins.
>>>> Please compile with plug-in support if you want to read non-GROMACS
>>>> trajectory formats.
>>>>
>>>>
>>>>
>>>> ### compilation was via nohup ./cn_compile.sh , where the contents of
>>> that
>>>> compilation script are:
>>>> mkdir -p ../../../exec/gromacs-5.1.2/serial_plugins
>>>> export FFTW_LOCATION=/scratch/cneale/exe/FFTW/fftw-3.3.4/exec
>>>> /scratch/cneale/exe/CMAKE/cmake-3.5.1-Linux-x86_64/bin/cmake
>>>> ../../../source/gromacs-5.1.2/ \
>>>> -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
>>>>
>>>>
>> -DCMAKE_INSTALL_PREFIX=$(pwd)/../../../exec/gromacs-5.1.2/serial_plugins
>>> \
>>>> -DGMX_X11=OFF \
>>>> -DGMX_MPI=OFF \
>>>> -DCMAKE_CXX_COMPILER=g++ \
>>>> -DCMAKE_C_COMPILER=gcc \
>>>> -DGMX_PREFER_STATIC_LIBS=ON \
>>>> -DGMX_GPU=OFF \
>>>> -DGMX_USE_PLUGINS=ON \
>>>>
>>>>
>>>
>> -DGMX_VMD_PLUGIN_PATH=/scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
>>>> make -j 8
>>>> make install -j 8
>>>>
>>>>
>>>>
>>>> ### I also tried adding the following preliminary command, but it made
>> no
>>>> difference:
>>>> export
>>>>
>> VMD_PLUGIN_PATH=/scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
>>>>
>>>> Also, including -DGMX_LOAD_PLUGINS=ON to the cmake command did not help
>>>> either.
>>>>
>>>>
>>>> ### Here is some further information that might be useful based on the
>>>> other posts I saw on this topic:
>>>>
>>>> $ grep PLUG CMakeCache.txt
>>>> GMX_LOAD_PLUGINS:BOOL=ON
>>>> GMX_USE_PLUGINS:UNINITIALIZED=ON
>>>>
>>>>
>>>
>> GMX_VMD_PLUGIN_PATH:UNINITIALIZED=/scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
>>>> //ADVANCED property for variable: GMX_LOAD_PLUGINS
>>>> GMX_LOAD_PLUGINS-ADVANCED:INTERNAL=1
>>>>
>>>> $ grep DLOPEN CMakeCache.txt
>>>> HAVE_DLOPEN:INTERNAL=1
>>>>
>>>> $ grep HAVE_DLOPEN nohup.out
>>>> -- Performing Test HAVE_DLOPEN
>>>> -- Performing Test HAVE_DLOPEN - Success
>>>>
>>>> $ ls /scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
>>>> abinitplugin.so brixplugin.so dcdplugin.so fs4plugin.so
>>>> jsplugin.so molemeshplugin.so pbeqplugin.so rst7plugin.so
>>>> vaspchgcarplugin.so webpdbplugin.so
>>>> avsplugin.so carplugin.so dlpolyplugin.so gamessplugin.so
>>>> lammpsplugin.so msmsplugin.so pdbplugin.so situsplugin.so
>>>> vaspoutcarplugin.so xbgfplugin.so
>>>> babelplugin.so ccp4plugin.so dmsplugin.so graspplugin.so
>>>> maeffplugin.so namdbinplugin.so phiplugin.so spiderplugin.so
>>>> vaspparchgplugin.so xsfplugin.so
>>>> basissetplugin.so corplugin.so dsn6plugin.so grdplugin.so
>>>> mapplugin.so netcdfplugin.so pltplugin.so stlplugin.so
>>>> vaspposcarplugin.so xyzplugin.so
>>>> bgfplugin.so cpmdplugin.so dtrplugin.so gridplugin.so
>>>> mdfplugin.so offplugin.so pqrplugin.so tinkerplugin.so
>>>> vaspxdatcarplugin.so
>>>> binposplugin.so crdplugin.so dxplugin.so gromacsplugin.so
>>>> mol2plugin.so parm7plugin.so psfplugin.so uhbdplugin.so
>>>> vaspxmlplugin.so
>>>> biomoccaplugin.so cubeplugin.so edmplugin.so hoomdplugin.so
>>>> moldenplugin.so parmplugin.so raster3dplugin.so
>>>> vasp5xdatcarplugin.so vtfplugin.so
>>>>
>>>>
>>>> Thank you for your advice on this compilation with plugins,
>>>> Chris.
>>>> --
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>>>>
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>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 23 Nov 2016 17:59:55 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Strange in PMF calculation (Shi Li)
> Message-ID: <20f5c35e-7cfb-8b03-e71b-0042a4b48e54 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
> Please don't reply to the entire digest.
>
> On 11/22/16 7:29 PM, Shi Li wrote:
>
>>> On 11/22/16 3:14 PM, Li, Shi wrote:
>>>> Dear Gromacs users,
>>>>
>>>> I am doing some PMF simulations of 2 molecules in vacuum and my resulting
>>>> profile has a strange look. I attached an eps files here, anyone can give
>>>> me some suggestion on why there is fluctuation at longer distance?
>>>>
>>>
>>> The mailing list does not accept attachments. Upload an image to a file-sharing
>>> service and provide the URL.
>>>
>>> -Justin
>>>
>>
>> Thank you Justin,
>>
>> Here is the link to my eps file.
>> https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0 <https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0>
>>
>
> Do you have sufficient sampling? How is the overlap between the histograms?
> This could just be a small sampling defect.
>
> -Justin
>
Thank you Justin,
The histogram plot is here: https://www.dropbox.com/s/0pcwpzulf5ezgv6/histo.png?dl=0 <https://www.dropbox.com/s/0pcwpzulf5ezgv6/histo.png?dl=0>
The beginning of this seems fine, each sample window was 0.05 nm from each other. I have done several systems with this .mdp and they worked fine. I don’t know why this one is different. It is a small molecule anyway, only 30 atoms each and the backbone is about 1.5 nm long.
Do you think I should decrease the distance between each sample window?
Shi
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
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