Re: [gmx-users] constant x-y plane area for membrane simulations.
On 1/30/20 8:21 PM, Miro Astore wrote: Hello all, I'm just wondering if gromacs supports constant x-y plane area for npt simulations like NAMD does. Use semiisotropic coupling with the x/y compressibility set to zero. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] constant x-y plane area for membrane simulations.
Hello all, I'm just wondering if gromacs supports constant x-y plane area for npt simulations like NAMD does. Best, Miro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Dear Szilárd, Thank you so much for your help. I performed the following steps and it seems to have built successfully, I'll let you know if it does not run correctly as well. rm -r gromacs-2020/ sudo apt-get install gcc-8 g++-8 tar -xvzf gromacs-2020.tar.gz cd gromacs-2020/ mkdir build cd build CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release make make check sudo make install source /usr/local/gromacs/bin/GMXRC Lastly, when I was building in default and ran into trouble I like to build in debug so it gives details about building and helps me identify source of the problems or identify relevant information to pass to you so you can better help me. I appreciate your comment about not building in debugging mode, but is there a way to run release in verbose mode? When I had problems with other programs I'd usually build my first time in debugger mode so I can monitor the process, then make clean and rebuild in default. Is there a better way to do this? Once again you help was greatly appreciated, Ryan PS again a few notes (if you have time to comment on anything incorrect) I have for people needing a fix in the future and maybe myself if I do this again in a few years and forget how. CUDA version (nvcc --version) is 9.1. This is a little confusing to me because you referenced CUDA 10.1 and I completely rebuilt this computer in September 2019, so unless there is a new driver since then it should be 10.1? I grabbed the newest drivers I could find but my computer is outputting 9.1 so I guess that is my version. when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails with the original error message regarding glibc 23.2. CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8 -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release Do you know why this is? When I started this adventure I just had sudo apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and specified the version in the build step, which failed. after taking that out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but fails in "make". Based on your suggestions I ran the commands at the top of the email to which then worked. Would this have worked if I had just installed gcc-8 g++-8 from the beginning and ran CMAKE with no version specification? On Thu, Jan 30, 2020 at 5:50 AM Szilárd Páll wrote: > Dear Ryan, > > On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz wrote: > > > Dear Szilárd, > > > > Thank you for your quick response. You are correct, after > > issuing sudo apt-get install gcc-9 g++-9 CMake was run with: > > > > gcc 9 is not supported with CUDA, as far as I know version 8 is the latest > supported gcc in CUDA 10.2 (officially "native support" whatever they mean > by that is for 7.3 on Ubuntu 18.04.3, see > https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug > > > > Don't use a Debug build unless you want to debug the GROMACS tools (it's > slow). > > Make sure that you cmake configuration does actually use the gcc version > you intend to use. The default invocation as above will pick up the default > compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by > opening the CMakeCache.txt file or using ccmake) -- and I think the lack of > proper AVX512 support in your default gcc 5 (which you are stil; using) is > the source of the issues you report below. > > You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the > configure step; for details see > > http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation > > Cheers, > -- > Szilárd > > > > However now I'm getting an error in make > > > > make VERBOSE=1 > > > > error: > > > > [ 25%] Building CXX object > > > > > src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o > > In file included from > > > > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0, > > from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146, > > from > > > > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40, > > from > > > > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49: > > > > >
Re: [gmx-users] Customize gromac FF for lipid parameters
On 1/30/20 3:02 PM, Yogesh Sharma wrote: Hey everyone, I have a membrane patch generated by charmm gui. I want to customize my gromac forcefield in accordance with it. I want some suggestion in extracting information from charmmff. I guess i need information to add in ffbonded and ffnonbonded files. Can someone help me with it I don't want to run simulations in charmmff I don't understand what you're trying to do. You want to add parameters to the CHARMM force field but you don't want to use CHARMM? If you want to use different parameters or a different force field, don't hack an existing one. There's no reason to do that. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Customize gromac FF for lipid parameters
Hey everyone, I have a membrane patch generated by charmm gui. I want to customize my gromac forcefield in accordance with it. I want some suggestion in extracting information from charmmff. I guess i need information to add in ffbonded and ffnonbonded files. Can someone help me with it I don't want to run simulations in charmmff -- * with regards* *Yogesh Sharma* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding rdf and number of molecules in the FSS of tetramer
Dear user's I have calculated the rdf of urea molecules around the peptides for different concentration of urea and obtained that peak height of first solvation shell (FSS) decreases with increase in concentration of urea. After that I have calculated the number of urea molecules in FSS and found that urea molecules in the FSS increases with concentration of urea. There is no correlation between the peak height of FSS and number of urea molecules. Can anybody suggest me ? what is the reason The command I have used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com -seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select "resname URE and within 0.5 of group protein" -selrpos whole_res_com -seltype whole_res_com -- Ashma Khan Research Scholar Department of Chemistry AMU, Aligarh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Analysis with .sh file
> > > Dear all, > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > and I found out that now that while I'm trying to use a .sh, as I was > doing in the version 5.0.4, now I'm receiving back an error since the > syntax is wrong. I'm wondering if someone could please help me. > > What is the script in your .sh file? There is not enough information to find out what goes wrong. > Regards, > > Riccardo > > > > -- > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 3D monitors
Hi all..Am looking for some good 3D monitors (either passive or active)Need suggestions for some good 3D monitors for protein structure and interactions visualization... with best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Charmm to Gromacs itps
On 1/28/20 3:35 AM, atb files wrote: @Justin: the lipid is not yet added to the charmm directory. Any script? How did you produce the original PSF? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] choice of ?Qm Optimized Energy
On 1/28/20 1:38 AM, Yogesh Sharma wrote: thanks for your response Dr. Justin these all values are for same ligand submitted under different molid. All have net zero charge. only difference is in dQm optimized energy. I dont know weather i have to choose one with lowest value or the highest. Please check the link attached https://atb.uq.edu.au/molecule.py?molid=364968 I don't have much experience with ATB but it appears that you're simply presented with alternate conformers that may be of lower energy. They're all very close in value so I don't know how you might use that information. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Analysis with .sh file
What is the command that causes the error and is the error due to incorrect syntax for bash or gromacs? No one will be able to help without more information. - John > Dear all, > > I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 > and I found out that now that while I'm trying to use a .sh, as I was > doing in the version 5.0.4, now I'm receiving back an error since the > syntax is wrong. I'm wondering if someone could please help me. > > Regards, > > Riccardo > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Analysis with .sh file
Dear all, I have recently upgrade my Gromacs to the 2019 version from the 5.0.4 and I found out that now that while I'm trying to use a .sh, as I was doing in the version 5.0.4, now I'm receiving back an error since the syntax is wrong. I'm wondering if someone could please help me. Regards, Riccardo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Dear Ryan, On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you for your quick response. You are correct, after > issuing sudo apt-get install gcc-9 g++-9 CMake was run with: > gcc 9 is not supported with CUDA, as far as I know version 8 is the latest supported gcc in CUDA 10.2 (officially "native support" whatever they mean by that is for 7.3 on Ubuntu 18.04.3, see https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug > Don't use a Debug build unless you want to debug the GROMACS tools (it's slow). Make sure that you cmake configuration does actually use the gcc version you intend to use. The default invocation as above will pick up the default compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by opening the CMakeCache.txt file or using ccmake) -- and I think the lack of proper AVX512 support in your default gcc 5 (which you are stil; using) is the source of the issues you report below. You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the configure step; for details see http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation Cheers, -- Szilárd > However now I'm getting an error in make > > make VERBOSE=1 > > error: > > [ 25%] Building CXX object > > src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o > In file included from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0, > from > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146, > from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40, > from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49: > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h: > In function ‘void gmx::gatherLoadTransposeHsimd(const float*, const float*, > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2; > int32_t = int]’: > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28: > error: the last argument must be scale 1, 2, 4, 8 > tmp1 = _mm512_castpd_ps( > ^ > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28: > error: the last argument must be scale 1, 2, 4, 8 > tmp2 = _mm512_castpd_ps( > ^ > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target > > 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o' > failed > make[2]: *** > > [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o] > Error 1 > CMakeFiles/Makefile2:2910: recipe for target > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > Makefile:162: recipe for target 'all' failed > make: *** [all] Error 2 > > after doing a 1 hour google I found discussions saying that the error > (Makefile:162: recipe for target 'all' failed) is too vague with no general > solution. I found fixes for headers and other files for other programs but > not fixes for this file. The fix linked below is for gromacs-2018 and a > different file but the general problem seems to suggest it still is a > gcc/g++ version compatibility error correct? Any suggestions for this > error? > > https://redmine.gromacs.org/issues/2312 > > > Thank you so much, > > Ryan > > PS Just to document for anyone else going through what I did for > Gromacs-2020 these were my steps. > > sudo apt-get install gcc g++ > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > > I then received multiple errors complaining about nvcc/C++ > incompatibility. After researching found errors for previous gromacs > versions suggesting to use gcc-5 (but as you suggested this error has been > patched). > > sudo apt-get install gcc-5 g++-5 > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5 > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5 > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug > -D_FORCE_INLINES=OFF > > Received different error described in previous email and solved with your > suggested solution. The key might be to specifically install latest version > number i.e. > > sudo apt-get install gcc-X
Re: [gmx-users] TraPPE-EH in GROMACS
Hi Maybe the definitions in the manual page (middle part) below may help you. ( http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=file%20top ) Best regards Alessandra On Tue, Jan 28, 2020 at 8:41 AM Dhrubajyoti Maji wrote: > Dear gromacs users, > I want to use TraPPE-EH force field parameters in GROMACS-2018.3. I > have understood that in top file nbfunc=1, > comb-rule=2,fudgeLJ=0.5,fudgeQQ=0.8333. But what will be the values of > gen-pairs, nrexcl and [ pairs] section ? Any kind of help will be highly > appreciated. > Thanks and regards > > Dhrubajyoti Maji > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to use TIP4P-ICE water model
Dear all, I want to use TIP4P-ICE water model for my simulations, but inbuilt .gro file of TIP4P-ICE is not available in Gromacs 2018. I tried alternate method by solvating using TIP4P model and then by changing the "itp" file of TIP4P in topology file with that of TIP4P-ICE. But the result of this simulation(RDF) is very different from that of literature. Please suggest any alternate approach. Thanks & Regards, Mangesh Bhendale -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
