Re: [gmx-users] Generation of the Distance Restraints
2) Also I've found that there is more simple way to define restraines based on the BONDS enty in the topology file. Could you provide me with the more information about this simpler way ? Simpler, but not a restraint to within a region. The manual section we are discussing links you to the available documentation elsewhere in the manual. I don't have the time to help with every interpretation question you might have. Mark Mark, In more details I want to generate network of disres for all helices H-bonds. So I want to restraint H-bond distance between i and i+4 atoms of the backbone. What is the simplest way to do such task? I think that the ussage of genrestr -disre could be useful for such generation of the complex disres because of the size of my protein. But how I could define the restrained atoms (i, i+4 atoms ) ? In the make_ndx options I didnt find the most trivial sollution of the such choise. So the only sollution is to define each I and I+4 atoms of the backbone manualy, isnt it ? James -- 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] Generation of the Distance Restraints
On 16/03/2012 6:39 PM, James Starlight wrote: 2) Also I've found that there is more simple way to define restraines based on the BONDS enty in the topology file. Could you provide me with the more information about this simpler way ? Simpler, but not a restraint to within a region. The manual section we are discussing links you to the available documentation elsewhere in the manual. I don't have the time to help with every interpretation question you might have. Mark Mark, In more details I want to generate network of disres for all helices H-bonds. So I want to restraint H-bond distance between i and i+4 atoms of the backbone. What is the simplest way to do such task? I think that the ussage of genrestr -disre could be useful for such generation of the complex disres because of the size of my protein. But how I could define the restrained atoms (i, i+4 atoms ) ? In the make_ndx options I didnt find the most trivial sollution of the such choise. So the only sollution is to define each I and I+4 atoms of the backbone manualy, isnt it ? Solving that will require some scripting. Because you know from genrestr -h that a half a matrix of distance restraints are generated for the index group chosen, and you only want i-i+4 restraints, you'll need a separate index group for every i-i+4 pair. So you can write a script that loops over calls to make_ndx to create a group of 2 atoms that are a suitable atom from i and i+4. Making make_ndx non-interactive (to call it from a script) is described on the website. Making a shell script to do that is a skill you will need to learn elsewhere. Mark -- 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] g_sas
Hi, Thanks dear Justin for useful reply, I have a system that is contained of protein-water-ions. I want to calculate residue SAS of protein. In the first way, I select a group consisting protein for calculation, and then this protein for output. At the second way, I select the whole system first for calculation, and then protein for output. The SAS_calculations of residue protein are different in two ways. I have two questions. Q1- Why results are different in two ways? Q2-Can anyone demonstrates clearly how residue SAS of protein calculate in two ways? Q3- what property or quantity do I can get from The SAS_calculations of residue protein in two ways? Best wishes, Afsaneh On 3/15/12, Justin A. Lemkul jalem...@vt.edu wrote: afsaneh maleki wrote: Hello dear user, I have a system that is contained protein-water-ions. I used the following command: g_sas -f free.xtc -s free.tpr -o area -or res_area -oa atom_area –q -nopbc I select the whole protein first for calculation, and then this protein for output.In this way I can obtain Area per residue from res_area file and area per atom from atom_area file. How to get area per residue with data of area per atom from atom_area file? When I average on area per atoms for a selected residue, it doesn't correspond with area per residue for a selected residue from res_area. It shouldn't. Averaging the areas per atom should not produce anything related to the constituent residue(s). The sum of the atom areas should yield the residue area. A quick look through the code seems to indicate that this is true, that is, the two quantities are not produced independently; residue area arises from atom area. -Justin How to correlate area per residue for a selected residue with area per atoms for a selected residue? Thanks in advance, Afsaneh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- 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] Scaling/performance on Gromacs 4
Hi Sara, The bad performance you are seeing is most probably caused by the combination of the new AMD Interlagos CPUs, compiler, operating system and it is very likely the the old Gromacs version also contributes. In practice these new CPUs don't perform as well as expected, but that is partly due to compilers and operating systems not having full support for the new architecture. However, based on the quite extensive benchmarking I've done, the with such a large system should be considerably better than what your numbers show. This is what you should try: - compile Gromacs with gcc 4.6 using the -march=bdver1 optimization flag; - have at least 3.0 or preferably newer Linux kernel; - if you're not required to use 4.0.x, use 4.5. Note that you have to be careful with drawing conclusions from benchmarking on small number of cores with large systems; you will get artifacts from caching effects. And now a bit of fairly technical explanation, for more details ask Google ;) The machine you are using has AMD Interlagos CPUs based on the Bulldozer micro-architecture. This is a new architecture, a departure from previous AMD processors and in fact quite different from most current CPUs. Bulldozer cores are not the traditional physical cores. In fact the hardware unit is the module which consists of two half cores (at least when it comes to floating point units). and enable a special type of multithreading called clustered multithreading. This is slightly similar to the Intel cores with Hyper-Threading. Cheers, -- Szilárd On Mon, Feb 20, 2012 at 5:12 PM, Sara Campos srrcam...@gmail.com wrote: Dear GROMACS users My group has had access to a quad processor, 64 core machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores) and I made some performance tests, using the following specifications: System size: 299787 atoms Number of MD steps: 1500 Electrostatics treatment: PME Gromacs version: 4.0.4 MPI: LAM Command ran: mpirun -ssi rpi tcp C mdrun_mpi ... #CPUS Time (s) Steps/s 64 195.000 7.69 32 192.000 7.81 16 275.000 5.45 8 381.000 3.94 4 751.000 2.00 2 1001.000 1.50 1 2352.000 0.64 The scaling is not good. But the weirdest is the 64 processors performing the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC and I do not understand why this is happening. Can anyone help? Thanks in advance, Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 4.6 development version
The docs actually tells you: Native GPU acceleration is supported with the verlet cut-off scheme (not with the group scheme) with PME, reaction-field, and plain cut-off electrostatics. (http://www.gromacs.org/Documentation/Parallelization_and_acceleration#GPU_acceleration) Use the cutoff-scheme = verlet mdp option, but before you start number crunching make sure to read the docs carefully! Cut-off schemes: http://www.gromacs.org/Documentation/Cut-off_schemes -- Szilárd On Thu, Mar 15, 2012 at 10:33 AM, SebastianWaltz sebastian.wa...@physik.uni-freiburg.de wrote: Dear Gromacs user, since a few days we try to get the heterogeneous parallelization on a Dell blade server with Tesla M2090 GPUs to work using the worksheet on the page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization we only get the OpenMM pure GPU version with mdrun-gpu running. Actually is the heterogeneous parallelization already working in the development version you can download using the link on the page: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6 and how can we get it running? Just adding the CMake variable GMX_GPU=ON when compiling mdrun did not enable the heterogeneous parallelization. We want to use the heterogeneous parallelization used in the 4.6 version to find out which is the optimal GPU/CPU ratio for our studied systems, since we soon have to buy machines for the upgrade of our cluster. Thanks a lot yours Sebastian -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas
afsaneh maleki wrote: Hi, Thanks dear Justin for useful reply, I have a system that is contained of protein-water-ions. I want to calculate residue SAS of protein. In the first way, I select a group consisting protein for calculation, and then this protein for output. At the second way, I select the whole system first for calculation, and then protein for output. The SAS_calculations of residue protein are different in two ways. I have two questions. Q1- Why results are different in two ways? You're asking g_sas to do two different things. You should note that g_sas tells you precisely how to do the calculation (from g_sas -h): The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. Choosing the whole system for the calculation group is wrong and will give an answer that is likely not what is needed. Q2-Can anyone demonstrates clearly how residue SAS of protein calculate in two ways? Refer to the literature cited in the g_sas screen output. Those papers will contain the methods. Your second method is, however, not appropriate. The first method is. Q3- what property or quantity do I can get from The SAS_calculations of residue protein in two ways? Likely a meaningful one and a useless one. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Announcement: Large biomolecule benchmark report
Thanks a a lot to you and also to Szilárd for your feedback and encouragement. I am very happy to see that this work is indeed useful especially to developers. We have no plans to make this into a 'proper' publication. I am not sure how much interested the simulation community would be because, to be honest, I have no overview what has been done in this area (besides the few benchmarks studies I have cited). Thanks again, Hannes. On Thu, 15 Mar 2012 22:02:21 +0100 David van der Spoel sp...@xray.bmc.uu.se wrote: On 2012-03-15 14:37, Hannes Loeffler wrote: Dear all, we proudly announce our third benchmarking report on (large) biomolecular systems carried out on various HPC platforms. We have expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS, LAMMPS and NAMD) and to five protein and protein-membrane systems ranging from 20 thousand to 3 million atoms. Please find the report on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx where we also offer the raw runtime data. We also plan to release the complete joint benchmark suite at a later date (as soon as we have access to a web server with sufficient storage space). We are open to any questions or comments related to our reports. It looks very interesting, and having benchmarks done by independent researchers is the best way to avoid bias. The differences are quite revealing, but it's also good that you point to problems compiling gromacs. Is this going to be submitted for publication somewhere too? Thanks for doing this, it must have been quite a job! Kind regards, Hannes Loeffler STFC Daresbury -- Scanned by iCritical. -- 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] Structural features for LINCS application
Il 16/03/2012 01:38, Mark Abraham ha scritto: On 16/03/2012 6:02 AM, Francesco Oteri wrote: Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Coupled constraints, such as you might have in a cluster, can be delicate. Equilibrating with a quite small time step can be necessary. Mark Hi Mark, I've run 100ps at 0.5fs, and 1fs...but when I switch to 2fs it crashes. I've read in the manual and it seem that triangular structures might introduce problem, but I dont have such a structure in my protein. So, there are other coupled constraint that may cause problem in LINCS? Is it possible that the force constants can cause problem? Or anyway, is it possible using virtual site constraining only h-bonds? Francesco -- 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] Simulated Annealing Protocol...
Dear Gromacs Specialists, I am very novice to Molecular Simulation study. I am using GROMACS 4.5.4 version . I completed some GROMACS tutorials , I not found any tutorial on Simulated Annealing.. If Any one know the link please give me it.. I make my protocol to work on simulated annealing as follow ... (I am not writing in detail sorry for that ) 1. pdb2gmx ... 2. editconf 3. Solvent Addition 4. Ion addition 5. Energy minimisation 6. simulated annealing mdp for simulated annealing is as follow... ; 7.3.3 Run Control title = simulated run integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 500 10 ns comm_mode = Linear; remove center of mass translation comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 100 ; [steps] freq to write coordinates to trajectory nstvout = 100 ; [steps] freq to write velocities to trajectory nstfout = 100 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 100 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 500 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.0 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.0 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.4 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.16 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = berendson ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 5 5 ; [K] reference temperature for coupling annealing = single single annealing_npoint= 2 2 annealing_time = 0 20 0 20 annealing_temp = 5 333 5 333 ; 7.3.15 Pressure Coupling pcoupl = parrinello-Rahman; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = yes ; velocity generation turned off gen_temp= 5 ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation = yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter= 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain My Queries 1. Is My mdp file ok ???..please give me a nice protocol.. 2.. Should I have to do position restrained MD before SA(simulated annealing) (If yes then what the temp. should I have to used for NVT and NPT (as in mdp file has lower 5 K and high 300 k ) ) -- gmx-users
Re: [gmx-users] tpbconv and tpr file problem...
On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: Hi Users: I was trying to calculate the energy contribution of an specific ion in my simulation. After extract a given frame from the simulation, I recalculate the energies of this frame with mdrun -rerun. Then I used tpbconv and editconf to create a new gro file and a new tpr without the ion. I tried to run mdrun -rerun with this new files but the mdrun stops with the following error: Program mdrun, VERSION 4.5.5 Source code file: domdec_top.c, line: 744 Software inconsistency error: Not enough position restraint coordinates What could be the problem? Probably some [moleculetype] now has insufficient atoms to cope with its position restraints, which apparently weren't edited (correctly) by the tpbconv subset procedure. Any possible solution? Probably depends on your use of position restraints, which would have been a good thing to have included in your original post Thank for your answer and sorry for the missing information. The position restraint is acting on the protein backbone. Since has nothing to do with the ion, I dont understand why the error... Anthony Mark -- 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 (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] Simulated Annealing Protocol...
rama david wrote: Dear Gromacs Specialists, I am very novice to Molecular Simulation study. I am using GROMACS 4.5.4 version . I completed some GROMACS tutorials , I not found any tutorial on Simulated Annealing.. If Any one know the link please give me it.. I make my protocol to work on simulated annealing as follow ... (I am not writing in detail sorry for that ) 1. pdb2gmx ... 2. editconf 3. Solvent Addition 4. Ion addition 5. Energy minimisation 6. simulated annealing mdp for simulated annealing is as follow... ; 7.3.3 Run Control title = simulated run integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 500 10 ns comm_mode = Linear; remove center of mass translation comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 100 ; [steps] freq to write coordinates to trajectory nstvout = 100 ; [steps] freq to write velocities to trajectory nstfout = 100 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 100 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 500 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.0 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.0 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.4 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.16 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = berendson ; temperature coupling with Nose-Hoover ensemble tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 0.10.1; [ps] time constant for coupling ref_t = 5 5 ; [K] reference temperature for coupling annealing = single single annealing_npoint= 2 2 annealing_time = 0 20 0 20 annealing_temp = 5 333 5 333 ; 7.3.15 Pressure Coupling pcoupl = parrinello-Rahman; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = yes ; velocity generation turned off gen_temp= 5 ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm= LINCS ; LINear Constraint Solver continuation = yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter= 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30; [degrees] maximum angle that a bond can rotate before LINCS will complain My Queries 1. Is My mdp file ok ???..please give me a nice protocol.. It is a bad idea to generate velocities and use P-R pressure coupling at the same time. Such an approach is extremely fragile and your simulation is likely to crash. I assume that
Re: [gmx-users] tpbconv and tpr file problem...
On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote: On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: Hi Users: I was trying to calculate the energy contribution of an specific ion in my simulation. After extract a given frame from the simulation, I recalculate the energies of this frame with mdrun -rerun. Then I used tpbconv and editconf to create a new gro file and a new tpr without the ion. I tried to run mdrun -rerun with this new files but the mdrun stops with the following error: Program mdrun, VERSION 4.5.5 Source code file: domdec_top.c, line: 744 Software inconsistency error: Not enough position restraint coordinates What could be the problem? Probably some [moleculetype] now has insufficient atoms to cope with its position restraints, which apparently weren't edited (correctly) by the tpbconv subset procedure. Any possible solution? Probably depends on your use of position restraints, which would have been a good thing to have included in your original post Thank for your answer and sorry for the missing information. The position restraint is acting on the protein backbone. Since has nothing to do with the ion, I dont understand why the error... Anthony OK, so maybe tpbconv subsets don't work well with position restraints. You can probably do what you want with a suitable combination of energy groups and mdrun -rerun. Mark -- 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] tpbconv and tpr file problem...
Thanks On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote: On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: Hi Users: I was trying to calculate the energy contribution of an specific ion in my simulation. After extract a given frame from the simulation, I recalculate the energies of this frame with mdrun -rerun. Then I used tpbconv and editconf to create a new gro file and a new tpr without the ion. I tried to run mdrun -rerun with this new files but the mdrun stops with the following error: Program mdrun, VERSION 4.5.5 Source code file: domdec_top.c, line: 744 Software inconsistency error: Not enough position restraint coordinates What could be the problem? Probably some [moleculetype] now has insufficient atoms to cope with its position restraints, which apparently weren't edited (correctly) by the tpbconv subset procedure. Any possible solution? Probably depends on your use of position restraints, which would have been a good thing to have included in your original post Thank for your answer and sorry for the missing information. The position restraint is acting on the protein backbone. Since has nothing to do with the ion, I dont understand why the error... Anthony OK, so maybe tpbconv subsets don't work well with position restraints. You can probably do what you want with a suitable combination of energy groups and mdrun -rerun. Mark -- 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] Announcement: Large biomolecule benchmark report
You should absolutely publish this. it would be of great interest. You can mitigate your chances of running into problems with the overview by sending a version of the manuscript to the developers of each software and asking them to provide a short paragraph, each of which you could include in a final section of responses from the developers. A manuscript such as this (and indeed the information that you have already made available) will be very useful for many reasons. One reason is that when new PhD students start learning about simulations, they tend to use the package that has been adopted by their research group and trust the (probably biased and partially uninformed) statements of their senior colleagues. Chris. -- original message -- Thanks a a lot to you and also to Szilárd for your feedback and encouragement. I am very happy to see that this work is indeed useful especially to developers. We have no plans to make this into a 'proper' publication. I am not sure how much interested the simulation community would be because, to be honest, I have no overview what has been done in this area (besides the few benchmarks studies I have cited). Thanks again, Hannes. On Thu, 15 Mar 2012 22:02:21 +0100 David van der Spoel sp...@xray.bmc.uu.se wrote: [Hide Quoted Text] On 2012-03-15 14:37, Hannes Loeffler wrote: Dear all, we proudly announce our third benchmarking report on (large) biomolecular systems carried out on various HPC platforms. We have expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS, LAMMPS and NAMD) and to five protein and protein-membrane systems ranging from 20 thousand to 3 million atoms. Please find the report on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx where we also offer the raw runtime data. We also plan to release the complete joint benchmark suite at a later date (as soon as we have access to a web server with sufficient storage space). We are open to any questions or comments related to our reports. It looks very interesting, and having benchmarks done by independent researchers is the best way to avoid bias. The differences are quite revealing, but it's also good that you point to problems compiling gromacs. Is this going to be submitted for publication somewhere too? Thanks for doing this, it must have been quite a job! Kind regards, Hannes Loeffler STFC Daresbury -- Scanned by iCritical. -- 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] cluster analysis of flexible peptide trajectory
Dear GROMACS users, Obviously RMSD-based clustering is not the best approach to find frequently visited conformations of flexible peptides. The other approach would be to used backbone dihedral angles to cluster the frames (i.e. with g_dih). There are also several articles in the literature describing more sophisticated clustering techniques used for MD trajectories of flexible peptides (e.g. spectral clustering), yet I haven't found any program that implements these methods to cluster the frames of a trajectory. Could anyone please recommend me a program for cluster analysis of peptide MD trajectories? Thanks in advance, Thomas -- 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] Re: Simulated Annealing Protocol
I am very novice to Molecular Simulation study. I am using GROMACS 4.5.4 version . I completed some GROMACS tutorials , I not found any tutorial on Simulated Annealing.. If Any one know the link please give me it.. I make my protocol to work on simulated annealing as follow ... (I am not writing in detail sorry for that ) 1. pdb2gmx ... 2. editconf 3. Solvent Addition 4. Ion addition 5. Energy minimisation 6. simulated annealing mdp for simulated annealing is as follow... ; 7.3.3 Run Control title = simulated run integrator = md ; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.002 * 500 10 ns comm_mode = Linear ; remove center of mass translation comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 100 ; [steps] freq to write coordinates to trajectory nstvout = 100 ; [steps] freq to write velocities to trajectory nstfout = 100 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 100 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 500 ; [real] precision to write xtc trajectory xtc_grps = System ; group(s) to write to xtc trajectory energygrps = System ; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 5 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.0 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb = 1.0 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw = 1.4 ; [nm] distance for LJ cut-off DispCorr = EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.16 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = berendson ; temperature coupling with Nose-Hoover ensemble tc_grps = Protein Non-Protein ; groups to couple seperately to temperature bath tau_t = 0.1 0.1 ; [ps] time constant for coupling ref_t = 5 5 ; [K] reference temperature for coupling annealing = single single annealing_npoint = 2 2 annealing_time = 0 20 0 20 annealing_temp = 5 333 5 333 ; 7.3.15 Pressure Coupling pcoupl = parrinello-Rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5 ; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = yes ; velocity generation turned off gen_temp = 5 ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm = LINCS ; LINear Constraint Solver continuation = yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30 ; [degrees] maximum angle that a bond can rotate before LINCS will complain My Queries 1. Is My mdp file ok ???..please give me a nice protocol.. 2.. Should I have to do position restrained MD before SA(simulated annealing) (If yes then what the temp. should I have to used for NVT
[gmx-users] AZH (AZIDOHOMOALANINE) or C4 H8 N4 O2
Dear Gromacs user, I am searching for the GROMOS (best would ffG53a5) forcefield parameters of the rather rarely used amino acid AZIDOHOMOALANINE (C4 H8 N4 O2). The residue looks like: http://www.chembase.com/cbid_147480.htm Every suggestion is very welcome since it can avoid doing the parametrization by my own saving me a lot of time. Sincerely Sebastian -- 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 installation question: Where is my Gromacs?
Dear all, I tried to install today Gromacs. I downloaded gromacs 4.5.5, Cuda, FFTW3. Installation of FFTW3 and Cuda went fine so far. I managed to execute sudo ./configure (in the gromacs untar folder). sudo make sudo make install make links did not work and I cannot find gromcas. There is no folder /usr/local/gromacs. I am a bit puzzled as I did install it. I am on MacOSx 10.6.7 and I used Terminal bash during the installation process. What can I do now to get Gromacs installed and running, please? Thank you. Kind regards Gudrun -- 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 installation question: Where is my Gromacs?
On 2012-03-16 20:19, bestenborstel wrote: Dear all, I tried to install today Gromacs. I downloaded gromacs 4.5.5, Cuda, FFTW3. Installation of FFTW3 and Cuda went fine so far. I managed to execute sudo ./configure (in the gromacs untar folder). sudo make sudo make install Try running again sudo make -n install it will not do anything, but in the terminal it will print where the program should be installed. make links did not work and I cannot find gromcas. There is no folder /usr/local/gromacs. I am a bit puzzled as I did install it. I am on MacOSx 10.6.7 and I used Terminal bash during the installation process. What can I do now to get Gromacs installed and running, please? Thank you. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 installation question: Where is my Gromacs?
bestenborstel wrote: Dear all, I tried to install today Gromacs. I downloaded gromacs 4.5.5, Cuda, FFTW3. Installation of FFTW3 and Cuda went fine so far. I managed to execute sudo ./configure (in the gromacs untar folder). sudo make The above steps do not need to be executed with sudo. sudo make install make links did not work and I cannot find gromcas. There is no folder /usr/local/gromacs. I am a bit puzzled as I did install it. When you say make links did not work, what happened? Was there are an error message of some sort? If your installation had been successful, you would indeed have a /usr/local/gromacs directory. The fact that it is not there suggests the installation did not actually work. Perhaps you missed an error message somewhere along the way. If I recall, /usr/local does not exist by default on Mac (I seem to remember having to create it myself). Perhaps that is an issue? If /usr/local doesn't exist, I don't know if Gromacs will create it or not. Just speculation there. -Justin I am on MacOSx 10.6.7 and I used Terminal bash during the installation process. What can I do now to get Gromacs installed and running, please? Thank you. Kind regards Gudrun -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 installation question: Where is my Gromacs?
Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. Thank you for your help. Kind regards Gudrun -- 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 installation question: Where is my Gromacs?
On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 installation question: Where is my Gromacs?
Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-) What do you ask me please to do? Am 16.03.2012 um 19:54 schrieb David van der Spoel: On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Gromacs installation question: Where is my Gromacs?
On 2012-03-16 21:03, bestenborstel wrote: Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-) What do you ask me please to do? sudo make install and check on the screen where the stuff is copied to. Am 16.03.2012 um 19:54 schrieb David van der Spoel: On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 installation question: Where is my Gromacs?
Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bin include lib share Gromacs finished again with: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. Do I have to execute 'make test' as the Gromacs page says test set is broken? Finally, is there something like 'make clean' to allow for a proper, clean re-installation? I thought I better ask again. Sorry. Gudrun Am 16.03.2012 um 20:05 schrieb David van der Spoel: On 2012-03-16 21:03, bestenborstel wrote: Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-) What do you ask me please to do? sudo make install and check on the screen where the stuff is copied to. Am 16.03.2012 um 19:54 schrieb David van der Spoel: On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Gromacs installation question: Where is my Gromacs?
bestenborstel wrote: Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bin include lib share Gromacs finished again with: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. You need sudo. It will write links into /usr/local/bin. It is not strictly necessary, as you can follow: http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation The GMXRC script magically configures your environment for you. Do I have to execute 'make test' as the Gromacs page says test set is broken? No, it won't do anything. Finally, is there something like 'make clean' to allow for a proper, clean re-installation? Yes. -Justin I thought I better ask again. Sorry. Gudrun Am 16.03.2012 um 20:05 schrieb David van der Spoel: On 2012-03-16 21:03, bestenborstel wrote: Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-) What do you ask me please to do? sudo make install and check on the screen where the stuff is copied to. Am 16.03.2012 um 19:54 schrieb David van der Spoel: On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 installation question: Where is my Gromacs?
Again 'sudo make links' gives: cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done Is this good or bad, please? g_luck is located for example now in /usr/local/bin/g_luck when I do 'which g_luck' Would you recommend to re-install, although it seems to work now? Thank you for your help. Thank you. Kind regards Gudrun Am 16.03.2012 um 20:28 schrieb Justin A. Lemkul: bestenborstel wrote: Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bininclude lib share Gromacs finished again with: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. You need sudo. It will write links into /usr/local/bin. It is not strictly necessary, as you can follow: http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation The GMXRC script magically configures your environment for you. Do I have to execute 'make test' as the Gromacs page says test set is broken? No, it won't do anything. Finally, is there something like 'make clean' to allow for a proper, clean re-installation? Yes. -Justin I thought I better ask again. Sorry. Gudrun Am 16.03.2012 um 20:05 schrieb David van der Spoel: On 2012-03-16 21:03, bestenborstel wrote: Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-) What do you ask me please to do? sudo make install and check on the screen where the stuff is copied to. Am 16.03.2012 um 19:54 schrieb David van der Spoel: On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive
Re: [gmx-users] Gromacs installation question: Where is my Gromacs?
bestenborstel wrote: Again 'sudo make links' gives: cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done Is this good or bad, please? In the absence of an error message, nothing is wrong. g_luck is located for example now in /usr/local/bin/g_luck when I do 'which g_luck' Would you recommend to re-install, although it seems to work now? I see no need for a reinstall. It appears to be working as expected. -Justin Thank you for your help. Thank you. Kind regards Gudrun Am 16.03.2012 um 20:28 schrieb Justin A. Lemkul: bestenborstel wrote: Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bin include lib share Gromacs finished again with: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Please run make tests now to verify your installation. If you want links to the executables in /usr/local/bin, you can issue make links now. Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. You need sudo. It will write links into /usr/local/bin. It is not strictly necessary, as you can follow: http://www.gromacs.org/Documentation/Installation_Instructions#Getting_access_to_GROMACS_after_installation The GMXRC script magically configures your environment for you. Do I have to execute 'make test' as the Gromacs page says test set is broken? No, it won't do anything. Finally, is there something like 'make clean' to allow for a proper, clean re-installation? Yes. -Justin I thought I better ask again. Sorry. Gudrun Am 16.03.2012 um 20:05 schrieb David van der Spoel: On 2012-03-16 21:03, bestenborstel wrote: Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-) What do you ask me please to do? sudo make install and check on the screen where the stuff is copied to. Am 16.03.2012 um 19:54 schrieb David van der Spoel: On 2012-03-16 20:49, bestenborstel wrote: Thank you for your quick reply. 'make links' produces: Saturn:gromacs-4.5.5 gudrun$ make links cd /usr/local/gromacs/bin programs=`ls` cd /usr/local/bin \ for i in $programs; do \ (test ! -f $i ln -s /usr/local/gromacs/bin/$i . ; exit 0); \ done /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory make: *** [links] Error 1 I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install' Sorry, I am not sure where to post this lengthy output. -n means not really run it without to install. But do you have permission to write in /usr/local? Thank you for your help. Kind regards Gudrun -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 -- Justin A.
[gmx-users] g_sas; could not find a Van der Waals radius
Hi, I have a system that is contained of Protein-DOPC-SOL-Ions. I want to calculate residue SAS of protein.The calculation group consists of all the non-solvent atoms in the system (37 residue Protein+ 125 DOPC+14 ion),and then protein for output. Force files used for protein and DOPC are ffg53a6 and Berger respectively. When I use g_sas I obtain the following message: WARNING: could not find a Van der Waals radius for 125 atoms. I have two questions. Q1- This warning is important? Q2-Is the valid source to get data for Van der Waals radius of phosphorous atom to insert in the vdwradii.dat file? I think this warning is about phosphorous atoms of DOPC. what is Van der Waals radius of phosphorous atoms that will be right for this goal? Thanks very much in advance, afsaneh -- 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] pdb2gmx error message
Dear All, I meet the following error message for pdb2gmx. Please let me know how to solve this problem. Cheers, Wholly Program pdb2gmx, VERSION 3.3.3 Source code file: futil.c, line: 542 Fatal error: Library file FF.dat not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable)-- 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] genion -pname no NA molecule (sodium) type
Dear All, I use the following to neutralize the charge genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8, Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr. However the feedback says there is no Na (sodium) moleculetype. I am looking forward to getting a reply from you on it, which is a fatal problem. Cheers, Wholly-- 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] genion -pname no NA molecule (sodium) type
On 17/03/2012 4:48 PM, Wholly Peach wrote: Dear All, I use the following to neutralize the charge genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8, Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr. However the feedback says there is no Na (sodium) moleculetype. Your force field defines [moleculetype] sections for ions in its ions.itp file. Go and look at it, compare with your .top and see what the problem is. Atom names, residue names and moleculetype names are all different things, and each part of your .top must match the right name at the right time. Mark -- 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] genion -pname no NA molecule (sodium) type
Will you please tell me where can I find the ions.itp file? I am looking forward to getting your reply. Wholly From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, 17 March 2012 3:55 PM Subject: Re: [gmx-users] genion -pname no NA molecule (sodium) type On 17/03/2012 4:48 PM, Wholly Peach wrote: Dear All, I use the following to neutralize the charge genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8, Then I do the following grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr. However the feedback says there is no Na (sodium) moleculetype. Your force field defines [moleculetype] sections for ions in its ions.itp file. Go and look at it, compare with your .top and see what the problem is. Atom names, residue names and moleculetype names are all different things, and each part of your .top must match the right name at the right time. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
