[gmx-users] Protein RMSD high
Dear All, While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 nm. I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Is it ok to report this problem with this RMSD value? Thanks Tarak -- 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] Protein RMSD high
Your call. Is that motion significant to what you are trying to report by your observation of the RMSD? Mark On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar tarak20...@gmail.com wrote: Dear All, While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 nm. I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Is it ok to report this problem with this RMSD value? Thanks Tarak -- 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 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] REMD
Wrong way around. Decide what you want to observe and how you will measure it *before* you do a simulation. Now you have a chance of doing the right simulation. On point, check out out chapter 8 of the manual. Mark On Thu, Jun 27, 2013 at 7:17 AM, Shine A shin...@iisertvm.ac.in wrote: Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- 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 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] Dear Sir
Fatal error: [ file spc.itp, line 32 ] Atom index (1) in bonds out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. in that case move the settles section to the right molecule the above error i am getting while running grommp command for membrane simulation. I made up the correct topology file.Here i used tip3p water model. But why this error coming i did not understood. Can you please clarify and suggest how to overcome this error. Regards M.SathishKumar -- 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] multiple chain restrain problem
Hello: I've got two protein chain in my system. I generate gmx.pdb by pb2gmx, and gromacs generate toplogy and restrain file for each chain: gmx.pdb topol_chain_A.itp topol_chain_B.itp porschain_A.itp porschain_B.itp I noticed that the gmx.pdb doesn't contain any chain information. I am going to equilibrate the system first restrain the heavy atoms which can be specified by porschain_A.itp and porschain_B.itp. However, in the next step I am going to restrain only the backbone of chain A, how can we to do this? The chain information in new generated gmx.pdb lost When I use command: genrestr -f gmx.pdb -p porsB it doesn't contains selection for chain thank you very much Albert -- 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] Installation on Ubuntu 12.04LTS
Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 Thanks in advance for your help, Al -- 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: Re: Re: [gmx-users] GPU-based workstation
Back to my question I want to build gpu-based workstation based onto 2 titans geforces. My current budget allow me only hight-end 6nodes core i 7-3930 and MB with 5 PCI-E (like Asus rampage IV series). Would this system be balanced with two GPUs ? Should I use two 6-8 nodes XEONS instead of i7? James 2013/5/29 James Starlight jmsstarli...@gmail.com Dear Dr. Pall! Thank you for your suggestions! Asumming that I have budget of 5000 $ and I want to build gpu-based desktop on this money. Previously I've used single 4 core i5 with GTX 670 and obtain average 10 ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites , sd integrator). Now I'd like to build system based on 2 hight-end GeForces (e.g like TITAN). Should that system include 2 cpu's for good balancing? (e.g two 6 nodes XEONS with faster clocks for instance could be better for simulations than i7, couldnt it?) What addition properties to the MB should I consider for such system ? James 2013/5/28 lloyd riggs lloyd.ri...@gmx.ch Dear Dr. Pali, Thank you, Stephan Watkins *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr *Von:* Szilárd Páll szilard.p...@cbr.su.se *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* Re: Re: [gmx-users] GPU-based workstation Dear all, As far as I understand, the OP is interested in hardware for *running* GROMACS 4.6 rather than developing code. or running LINPACK. To get best performance it is important to use a machine with hardware balanced for GROMACS' workloads. Too little GPU resources will result in CPU idling; too much GPU resources will lead to the runs being CPU or multi-GPU scaling bound and above a certain level GROMACS won't be able to make use of additional GPUs. Of course, the balance will depend both on hardware and simulation settings (mostly the LJ cut-off used). An additional factor to consider is typical system size. To reach near peak pair-force throughput on GPUs you typically need 20k-40k particles/GPU (depends on the architecture) and throughput drops below these values. Hence, in most cases it is preferred to use fewer and faster GPUs rather than more. Without knowing the budgdet and indented use of the machine it is hard to make suggestions, but I would say for a budget desktop box a quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well. If you're considering dual-socket workstations, I suggest you go with the higher core-count and higher frequency Intel CPUs (6+ cores 2.2 GHz), otherwise you may not see as much benefit as you would expect based on the insane price tag (especially if you compare to an i7 3939K or its IVB successor). Cheers, -- Szilárd On Sat, May 25, 2013 at 1:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: More RAM the better, and the best I have seen is 4 GPU work station. I can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot board really holds 8 or 10 GPU's). There's cooling problems though with GPU's, as on a board there packed, so extra cooling things may help not blow a GPU, but I would look for good ones (ask around), as its a video game market and they go for looks even though its in casing? The external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont know performance wise, the onboard GPU, the more RAM the marrier...so yes, normal work stations you can get 4 GPU's for a 300 US$ board, but then the price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests software, not Gromacs, so would be nice to see performance...for a small 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps eq's Stephan Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] GPU-based workstation Dear Dr. Watkins! Thank you for the suggestions! In the local shops I've found only Core i7 with 6 cores (like Core i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores than with 4 cores in case of i7 cpu (assuming that I run simulation in cpu+gpu mode )? Also you've mentioned about 4 PCeI MD. Does it means that modern work-station could have 4 GPU's in one home-like desktop ? According to my current task I suppose that 2 GPU's would be suitable for my simulations (assuming that I use typical ASUS MB and 650 Watt power unit). Have someone tried to use several GPU's on one workstation ? What attributes of MB
Re: [gmx-users] Dear Sir
On 6/27/13 5:59 AM, Sathish Kumar wrote: Fatal error: [ file spc.itp, line 32 ] Atom index (1) in bonds out of bounds (1-0). This probably means that you have inserted topology section settles in a part belonging to a different molecule than you intended to. in that case move the settles section to the right molecule the above error i am getting while running grommp command for membrane simulation. I made up the correct topology file.Here i used tip3p water model. But why this error coming i did not understood. Can you please clarify and suggest how to overcome this error. http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] multiple chain restrain problem
On 6/27/13 6:27 AM, Albert wrote: Hello: I've got two protein chain in my system. I generate gmx.pdb by pb2gmx, and gromacs generate toplogy and restrain file for each chain: gmx.pdb topol_chain_A.itp topol_chain_B.itp porschain_A.itp porschain_B.itp I noticed that the gmx.pdb doesn't contain any chain information. I am going to equilibrate the system first restrain the heavy atoms which can be specified by porschain_A.itp and porschain_B.itp. However, in the next step I am going to restrain only the backbone of chain A, how can we to do this? The chain information in new generated gmx.pdb lost When I use command: genrestr -f gmx.pdb -p porsB it doesn't contains selection for chain Then select by residue number. Note that genrestr will only work for the first molecule, since position restraint numbering is based on the [moleculetype] numbering, not the coordinate file numbering. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Installation on Ubuntu 12.04LTS
On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 CUDA 4.0 is two years old, so I would(did) get the latest package from Nvidia rather than rely on synaptic to be up to date with emerging technologies. And use a more recent gcc! Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: Yeah CUDA's wrapper compiler does not play perfectly with non-gcc, but the result should be OK. We have filed bug reports with CUDA. $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 On the other hand, FFTW development is nearly stopped, so libfftw3-dev from synaptic is fine, and I suspect the origin of this issue is either a race condition in the internal FFTW build (which will go away if you make again), or perhaps icc being evil and conveniently wrapping an FFTW interface over its MKL. We believe we've fixed the latter, but there are too many moving targets... Mark Thanks in advance for your help, Al -- 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 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] still dealing with GFP-like chromophore with LINCS warnings
Dear gmx-users, I'm still dealing with the problem of GFP-like chromophore. To be honest, with the help of another gmx user, I was able to obtain the topology of my chromophore, in protonated and unprotonated form, and I started performing the simulations. For the protonated chromophore, all worked well, and I obtained my simulations without many problems. Instead, I'm experimenting problems with the protein containing the unprotonated form. In particular, when I started calculating the production run, using in the .mdp files exactly the same parameters used for the protonated form, I started obtaining a lot of LINCS warnings and production of a lot of stepX.pdb files. This happened only during the production run, whereas I have no errors during minimization and position-restrained dynamics. The minimization step seems to be OK and I did not further continue with it (I set emtol=500 and emstep=0.01; the result of minimization was: Steepest Descents converged to Fmax 500 in 2114 steps Potential Energy= -6.84833590617959e+05 Maximum force=4.57025361763790e+02 on atom 2129 Norm of force=9.42624640937790e+00 that seems pretty good for me.) I tried to overcome the problem by using longer PR-MD (100 ps instead of 10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite the fact that the energies and all other factors (temperature, pressure) are really stable during PR-MD. I also watched the trajectory using VMD but, apart from parts of protein crossing periodic boundaries (a thing that I see regularly in my simulations), I don't see anything strange (like system exploding). Apparently, it simply stops, and that's all. Other things that trouble me are: 1) I checked the atoms with LINCS warning, and I see that not only those atoms belonging to chromophore are perturbed, but also other atoms in the backbone of the protein (mainly CA-C-N; many of them, but not all, are spatially close to chromophore). 2) during these production runs I also experimented many hardware problems (power outages) and software problems (bad job schedulation, problems in core communications etc) and I don't understand if these problems could affect the results of my simulation in this way. I ask this because my first production run was stopped because of a power outage, and in the .log file I saw a lot of errors very early; when the machine turned on, I resent exactly the same dynamics, and the errors were far later than before (in the first run, they came across 5 ns; in the second run not before 20 ns). 3) Last thing: when I started the production run, I switched the pressure coupling from Berendsen to Parrinello-Rahman (obviously not giving the .edr file to grompp for the creation of the full.tpr file) (on the contrary, the temperature coupling was left V-rescale both in PR-Md and production run). Can this switch perturb the system? My question is: do I have to suppose that the unprotonated form of chromophore is badly parametrized, and this can influence all the rest of the protein in this way? If yes, why nothing happens when I do PR-MD? If not, do I have simply to perform a very very very long stabilization, do I have to perform a deeper minimization, do I have to avoid switching from Berendsen to Parrinello? What do you suggest me to do? Thanks a lot Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index Indifference is the eighth deadly sin (don Andrea Gallo) -- 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] Visualize Protein ligand complex
Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions with protein binding site I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge with solvent molecules so pymol couldnot visualize complex Can anybody tell me command how to visualize protein ligand complex trajectory in pymol Thanks, Sainitin -- 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] Installation on Ubuntu 12.04LTS
On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero marelibe...@yahoo.com wrote: Hello everybody, Does anyone have any recommendation regarding the installation of gromacs 4.6 on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers 304.88. Apparently, this is not compatible with gcc-4.5 and higher. When I issue: $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON $ make the compilation ends with: In file included from /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, from command-line:0: /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! If I downgrade to gcc-4.4 this error disappears, but gromacs compilation fails with a different error: cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): Error generating /home/me/Downloads/gromacs-4.6.2/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 I guess what happens is that you are using gcc 4.5 for the CPU code and gcc 4.4 as the nvcc host compiler. However, the compiler options used for gcc (CMAKE_CXX_FLAGS) get propagated to nvcc; -fexcess-precision=fast is supported by gcc 4.5, but not by 4.4, hence the error when compiling CUDA code. Also, I tried the Intel compilers that comes with the non-commercial Intel c++ composer XE (which I believe are recommended). The compilation produces a number of warnings, and then dies with the following error: $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by `share/template/template'. Stop. make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 make: *** [all] Error 2 This should work, but CUDA 4.0 is ancient surely does not support icc 13. I suggest that you get CUDA 5.0 and use gcc 4.7 (or a new icc). If you really want to stick to CUDA 4.0, try using gcc 4.4 as the general C++ compiler (CMAKE_CXX_COMPILER) which should avoid the above error. Thanks in advance for your help, Al -- 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 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] Protein RMSD high
No, it's not at all significant in my problem as the loop is not part of the active site, way far at the two termini. I have plotted the RMSD in presence and absence of the loop. In absence of the loop rmsd is coming around 0.3 nm. Thanks Mark Tarak On Thu, Jun 27, 2013 at 2:37 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Your call. Is that motion significant to what you are trying to report by your observation of the RMSD? Mark On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar tarak20...@gmail.com wrote: Dear All, While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 nm. I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Is it ok to report this problem with this RMSD value? Thanks Tarak -- 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 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 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] Visualize Protein ligand complex
Don't you wanna try to use the VMD use vmd xxx.gro yyy.trr and then you could highlight your ligand 2013/6/27 Sainitin Donakonda saigr...@gmail.com Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions with protein binding site I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge with solvent molecules so pymol couldnot visualize complex Can anybody tell me command how to visualize protein ligand complex trajectory in pymol Thanks, Sainitin -- 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 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] still dealing with GFP-like chromophore with LINCS warnings
I did experience some troubles using Parrinello-Rahman after an equilibration with Berendsen. Trying many different time-constant was the solution ( I had to shift this constant from 10 ps for Berendsen to 5 ps for PR). Did you try to change it ? I do not know the fundamental reasons for this problem, though... Baptiste 2013/6/27 Anna Marabotti amarabo...@unisa.it Dear gmx-users, I'm still dealing with the problem of GFP-like chromophore. To be honest, with the help of another gmx user, I was able to obtain the topology of my chromophore, in protonated and unprotonated form, and I started performing the simulations. For the protonated chromophore, all worked well, and I obtained my simulations without many problems. Instead, I'm experimenting problems with the protein containing the unprotonated form. In particular, when I started calculating the production run, using in the .mdp files exactly the same parameters used for the protonated form, I started obtaining a lot of LINCS warnings and production of a lot of stepX.pdb files. This happened only during the production run, whereas I have no errors during minimization and position-restrained dynamics. The minimization step seems to be OK and I did not further continue with it (I set emtol=500 and emstep=0.01; the result of minimization was: Steepest Descents converged to Fmax 500 in 2114 steps Potential Energy= -6.84833590617959e+05 Maximum force=4.57025361763790e+02 on atom 2129 Norm of force=9.42624640937790e+00 that seems pretty good for me.) I tried to overcome the problem by using longer PR-MD (100 ps instead of 10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite the fact that the energies and all other factors (temperature, pressure) are really stable during PR-MD. I also watched the trajectory using VMD but, apart from parts of protein crossing periodic boundaries (a thing that I see regularly in my simulations), I don't see anything strange (like system exploding). Apparently, it simply stops, and that's all. Other things that trouble me are: 1) I checked the atoms with LINCS warning, and I see that not only those atoms belonging to chromophore are perturbed, but also other atoms in the backbone of the protein (mainly CA-C-N; many of them, but not all, are spatially close to chromophore). 2) during these production runs I also experimented many hardware problems (power outages) and software problems (bad job schedulation, problems in core communications etc) and I don't understand if these problems could affect the results of my simulation in this way. I ask this because my first production run was stopped because of a power outage, and in the .log file I saw a lot of errors very early; when the machine turned on, I resent exactly the same dynamics, and the errors were far later than before (in the first run, they came across 5 ns; in the second run not before 20 ns). 3) Last thing: when I started the production run, I switched the pressure coupling from Berendsen to Parrinello-Rahman (obviously not giving the .edr file to grompp for the creation of the full.tpr file) (on the contrary, the temperature coupling was left V-rescale both in PR-Md and production run). Can this switch perturb the system? My question is: do I have to suppose that the unprotonated form of chromophore is badly parametrized, and this can influence all the rest of the protein in this way? If yes, why nothing happens when I do PR-MD? If not, do I have simply to perform a very very very long stabilization, do I have to perform a deeper minimization, do I have to avoid switching from Berendsen to Parrinello? What do you suggest me to do? Thanks a lot Anna -- __** Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/**annamarabotti/indexhttp://www.unisa.it/docenti/annamarabotti/index Indifference is the eighth deadly sin (don Andrea Gallo) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
Re: [gmx-users] Visualize Protein ligand complex
Hi Sainitin, You can extract only the protein and ligand, using a suitable index file, or you can limit the number of frames. Cheers, Tsjerk On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger kronenberg...@gmail.com wrote: Don't you wanna try to use the VMD use vmd xxx.gro yyy.trr and then you could highlight your ligand 2013/6/27 Sainitin Donakonda saigr...@gmail.com Hi, I simulated protein ligand complex for 20 ns now i want to visualize this complex after simulation in pymol.To look ligand interactions with protein binding site I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too huge with solvent molecules so pymol couldnot visualize complex Can anybody tell me command how to visualize protein ligand complex trajectory in pymol Thanks, Sainitin -- 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 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] multiple chain restrain problem
On 06/27/2013 01:50 PM, Justin Lemkul wrote: Then select by residue number. Note that genrestr will only work for the first molecule, since position restraint numbering is based on the [moleculetype] numbering, not the coordinate file numbering. -Justin thank you very much for kind advices. I solved this by extracting each chain into indivisual coordinate and make restrain based on them. best Albert -- 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] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
Hello all, I have a naphthalene + water system which I want to run a NPT simulation of. The system has been energy mininimized. When I run the NPT simulation using gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same simulation using 4.5.4 it crashes with lincs error. We have tried various things like energy minimizing multiple times using 4.5.4 but it still crashes. I have also changed the thermostat and barostat to Berendsen, the problem persists. Has anything changed between the two versions that could lead to this trouble? I am pasted the mdp file below and also the last few lines of the error message I get from Gromacs 4.5.4. Thanks for your help. Sapna MDP FILE * title = NPH + water ; a string dt = 0.002; time step nsteps = 1250 ; number of steps comm-grps = system comm-mode = Linear nstcomm = 10 ; reset c.o.m. motion nstxout = 000 ; write coords nstvout = 000 ; write velocities nstlog = 2500 ; print to logfile nstenergy = 500 ; print energies xtc_grps= System nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.00 ; cut-off for vdw rcoulomb= 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 280.0 tc-grps = System tau_t = 0.5 DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 280 ; init. temp. gen_seed= 372340 ; random seed constraints = h-bonds ; constraining bonds with H constraint_algorithm = lincs refcoord-scaling= no Pcoupl = Parrinello-Rahman Pcoupltype = isotropic; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure nsttcouple = 1 nstpcouple = 1 * END MDP File *** *** Error Message * Program mdrun_sp, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (4811) 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 --- *** End Error Message * -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] clarification of equation 4.65
Dear Users: can anybody confirm that there is a mistake in equation 4.65 on page 82 of the manual for version 4.6.1? Specifically, I think that the final term should be C4*(1-cos(4*theta)) and not C4*(1+cos(4*theta)) where the difference is the sign of the cosine term ? Thank you, Chris. -- 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] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
On 6/27/13 2:30 PM, sarupria wrote: Hello all, I have a naphthalene + water system which I want to run a NPT simulation of. The system has been energy mininimized. When I run the NPT simulation using gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same simulation using 4.5.4 it crashes with lincs error. We have tried various things like energy minimizing multiple times using 4.5.4 but it still crashes. I have also changed the thermostat and barostat to Berendsen, the problem persists. Has anything changed between the two versions that could lead to this trouble? I am pasted the mdp file below and also the last few lines of the error message I get from Gromacs 4.5.4. Well, according to the release notes (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x), in version 4.5.5: Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. Small bugs are constantly getting fixed. I see no compelling reason to use an outdated version (4.5.4) when a slightly less outdated version (4.5.5) works correctly. -Justin Thanks for your help. Sapna MDP FILE * title = NPH + water ; a string dt = 0.002; time step nsteps = 1250 ; number of steps comm-grps = system comm-mode = Linear nstcomm = 10 ; reset c.o.m. motion nstxout = 000 ; write coords nstvout = 000 ; write velocities nstlog = 2500 ; print to logfile nstenergy = 500 ; print energies xtc_grps= System nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.00 ; cut-off for vdw rcoulomb= 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 280.0 tc-grps = System tau_t = 0.5 DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 280 ; init. temp. gen_seed= 372340 ; random seed constraints = h-bonds ; constraining bonds with H constraint_algorithm = lincs refcoord-scaling= no Pcoupl = Parrinello-Rahman Pcoupltype = isotropic; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure nsttcouple = 1 nstpcouple = 1 * END MDP File *** *** Error Message * Program mdrun_sp, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (4811) 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 --- *** End Error Message * -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
Thanks Justin for the response. I thought of that too but was not sure if that could alone be attributed to the crash. There is no obvious reason why it should happen given Gromacs has typically been quite stable. This is quite a straightforward system...but perhaps it is the version. I am able to run other simulations in this version with similar set up and therefore, I wonder what is going wrong. On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/13 2:30 PM, sarupria wrote: Hello all, I have a naphthalene + water system which I want to run a NPT simulation of. The system has been energy mininimized. When I run the NPT simulation using gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same simulation using 4.5.4 it crashes with lincs error. We have tried various things like energy minimizing multiple times using 4.5.4 but it still crashes. I have also changed the thermostat and barostat to Berendsen, the problem persists. Has anything changed between the two versions that could lead to this trouble? I am pasted the mdp file below and also the last few lines of the error message I get from Gromacs 4.5.4. Well, according to the release notes (http://www.gromacs.org/About_** Gromacs/Release_Notes/**Versions_4.5.xhttp://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x), in version 4.5.5: Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. Small bugs are constantly getting fixed. I see no compelling reason to use an outdated version (4.5.4) when a slightly less outdated version (4.5.5) works correctly. -Justin Thanks for your help. Sapna MDP FILE * title = NPH + water ; a string dt = 0.002; time step nsteps = 1250 ; number of steps comm-grps = system comm-mode = Linear nstcomm = 10 ; reset c.o.m. motion nstxout = 000 ; write coords nstvout = 000 ; write velocities nstlog = 2500 ; print to logfile nstenergy = 500 ; print energies xtc_grps= System nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.00 ; cut-off for vdw rcoulomb= 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 280.0 tc-grps = System tau_t = 0.5 DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 280 ; init. temp. gen_seed= 372340 ; random seed constraints = h-bonds ; constraining bonds with H constraint_algorithm = lincs refcoord-scaling= no Pcoupl = Parrinello-Rahman Pcoupltype = isotropic; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure nsttcouple = 1 nstpcouple = 1 * END MDP File *** *** Error Message * Program mdrun_sp, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (4811) 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/Errorshttp://www.gromacs.org/Documentation/Errors --**- *** End Error Message * -- View this message in context: http://gromacs.5086.x6.nabble.** com/Gromacs-4-5-4-and-Gromacs-**4-5-5-give-different-results-** tp5009424.htmlhttp://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
On 6/27/13 3:16 PM, Sapna Sarupria wrote: Thanks Justin for the response. I thought of that too but was not sure if that could alone be attributed to the crash. There is no obvious reason why it should happen given Gromacs has typically been quite stable. This is quite a straightforward system...but perhaps it is the version. I am able to run other simulations in this version with similar set up and therefore, I wonder what is going wrong. Without an actual backtrace from gdb, there's not much to go on, but then too, the development team isn't going to try to fix anything about 4.5.4 that presumably has already been fixed. The most obvious culprit in the .mdp file below is the combination of velocity generation and Nose-Hoover; it's not a very stable combination. -Justin On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/13 2:30 PM, sarupria wrote: Hello all, I have a naphthalene + water system which I want to run a NPT simulation of. The system has been energy mininimized. When I run the NPT simulation using gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same simulation using 4.5.4 it crashes with lincs error. We have tried various things like energy minimizing multiple times using 4.5.4 but it still crashes. I have also changed the thermostat and barostat to Berendsen, the problem persists. Has anything changed between the two versions that could lead to this trouble? I am pasted the mdp file below and also the last few lines of the error message I get from Gromacs 4.5.4. Well, according to the release notes (http://www.gromacs.org/About_** Gromacs/Release_Notes/**Versions_4.5.xhttp://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x), in version 4.5.5: Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. Small bugs are constantly getting fixed. I see no compelling reason to use an outdated version (4.5.4) when a slightly less outdated version (4.5.5) works correctly. -Justin Thanks for your help. Sapna MDP FILE * title = NPH + water ; a string dt = 0.002; time step nsteps = 1250 ; number of steps comm-grps = system comm-mode = Linear nstcomm = 10 ; reset c.o.m. motion nstxout = 000 ; write coords nstvout = 000 ; write velocities nstlog = 2500 ; print to logfile nstenergy = 500 ; print energies xtc_grps= System nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.00 ; cut-off for vdw rcoulomb= 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 280.0 tc-grps = System tau_t = 0.5 DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 280 ; init. temp. gen_seed= 372340 ; random seed constraints = h-bonds ; constraining bonds with H constraint_algorithm = lincs refcoord-scaling= no Pcoupl = Parrinello-Rahman Pcoupltype = isotropic; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure nsttcouple = 1 nstpcouple = 1 * END MDP File *** *** Error Message * Program mdrun_sp, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (4811) 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/Errorshttp://www.gromacs.org/Documentation/Errors --**- *** End Error Message * -- View this message in context: http://gromacs.5086.x6.nabble.** com/Gromacs-4-5-4-and-Gromacs-**4-5-5-give-different-results-** tp5009424.htmlhttp://gromacs.5086.x6.nabble.com/Gromacs-4-5-4-and-Gromacs-4-5-5-give-different-results-tp5009424.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --
Re: [gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results
I have tried the same with Berendsen and it still crashes. I have seen this happen before in some other versions compatibility too (I have an old post about it in the mailing list). Thanks for the response! On Thu, Jun 27, 2013 at 3:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/13 3:16 PM, Sapna Sarupria wrote: Thanks Justin for the response. I thought of that too but was not sure if that could alone be attributed to the crash. There is no obvious reason why it should happen given Gromacs has typically been quite stable. This is quite a straightforward system...but perhaps it is the version. I am able to run other simulations in this version with similar set up and therefore, I wonder what is going wrong. Without an actual backtrace from gdb, there's not much to go on, but then too, the development team isn't going to try to fix anything about 4.5.4 that presumably has already been fixed. The most obvious culprit in the .mdp file below is the combination of velocity generation and Nose-Hoover; it's not a very stable combination. -Justin On Thu, Jun 27, 2013 at 3:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/13 2:30 PM, sarupria wrote: Hello all, I have a naphthalene + water system which I want to run a NPT simulation of. The system has been energy mininimized. When I run the NPT simulation using gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same simulation using 4.5.4 it crashes with lincs error. We have tried various things like energy minimizing multiple times using 4.5.4 but it still crashes. I have also changed the thermostat and barostat to Berendsen, the problem persists. Has anything changed between the two versions that could lead to this trouble? I am pasted the mdp file below and also the last few lines of the error message I get from Gromacs 4.5.4. Well, according to the release notes (http://www.gromacs.org/About_** ** http://www.gromacs.org/About_** Gromacs/Release_Notes/Versions_4.5.xhttp://www.** gromacs.org/About_Gromacs/**Release_Notes/Versions_4.5.xhttp://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x )**, in version 4.5.5: Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. Small bugs are constantly getting fixed. I see no compelling reason to use an outdated version (4.5.4) when a slightly less outdated version (4.5.5) works correctly. -Justin Thanks for your help. Sapna MDP FILE * title = NPH + water ; a string dt = 0.002; time step nsteps = 1250 ; number of steps comm-grps = system comm-mode = Linear nstcomm = 10 ; reset c.o.m. motion nstxout = 000 ; write coords nstvout = 000 ; write velocities nstlog = 2500 ; print to logfile nstenergy = 500 ; print energies xtc_grps= System nstxtcout = 1000 nstlist = 10 ; update pairlist ns_type = grid ; pairlist method coulombtype = PME rvdw= 1.00 ; cut-off for vdw rcoulomb= 1.00 ; cut-off for coulomb rlist = 1.00 ; cut-off for coulomb Tcoupl = Nose-Hoover ref_t = 280.0 tc-grps = System tau_t = 0.5 DispCorr= EnerPres ; long range correction gen_vel = yes ; generate init. vel gen_temp= 280 ; init. temp. gen_seed= 372340 ; random seed constraints = h-bonds ; constraining bonds with H constraint_algorithm = lincs refcoord-scaling= no Pcoupl = Parrinello-Rahman Pcoupltype = isotropic; pressure geometry tau_p = 1.0 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; ref pressure nsttcouple = 1 nstpcouple = 1 * END MDP File *** *** Error Message * Program mdrun_sp, VERSION 4.5.4 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (4811) 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
[gmx-users] PBC problem
Hi all, I have a question about PBC. If I have a polymer chain that is longer than the box length, will the properties of the chain change because the tail of the chain may interact with the head of the chain due to PBC? Thank you! Yutian -- 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] clarification of equation 4.65
Seems plausible, but someone would have to double-check the trig. Or make a test case where theta is 0, and then see whether C4 changes the potential in a rerun (should be minus) or not (not). Code's in src/kernel/convparm.c. Mark On Thu, Jun 27, 2013 at 8:46 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Dear Users: can anybody confirm that there is a mistake in equation 4.65 on page 82 of the manual for version 4.6.1? Specifically, I think that the final term should be C4*(1-cos(4*theta)) and not C4*(1+cos(4*theta)) where the difference is the sign of the cosine term ? Thank you, Chris. -- 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 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] PBC problem
Hi Yutian Yang, Yes. That is, if the chain is interacting with itself. If it remains curled up, then it won't be a problem. Cheers, Tsjerk On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang yyan...@syr.edu wrote: Hi all, I have a question about PBC. If I have a polymer chain that is longer than the box length, will the properties of the chain change because the tail of the chain may interact with the head of the chain due to PBC? Thank you! Yutian -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Pulling
Dear users, I have a sytem including protein, lipids, and water. My protein is in center of the box. Now i want it stays at one side of the box. Which tool or command should i use to pull the protein to a any mong muốn location ? Thankful for any help ! Thu -- 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
