[gmx-users] grompp for minimization: note warning
Dear Justin Very thanks for your reply. You said I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check. I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. Based on your suggestion, I used -maxwarn option for grompp. Then I used -nt 1 option for mdrun, but this step takes too long and Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2122 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.4310875e+05 Maximum force = 2.7179752e+04 on atom 5271 Norm of force = 4.0253470e+02 -- my em.mdp file is as follows: integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions -- gro, edr, trr and lof file were created. I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp file, but result are the same. Is this minimization completely true? Can I use created gro file of this minimization for next step (equilibration)? I am beginner in gromacs, please help me to resolve this problem. Best wishes -- 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] question about installation parameters
Dear GMX users, I have a question about the combination of the installation parameters. I compiled the fftw lib with --enable-sse2 and configured the gromacs with cmake .. -DGMX_CPU_ACCELERATION=SSE4.1. I'd like to know if it is ok to use such a combination? Many thanks. Mingjun-- 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] question about installation parameters
Hi, On Sep 16, 2013, at 11:23 AM, mjyang mjy...@hku.hk wrote: Dear GMX users, I have a question about the combination of the installation parameters. I compiled the fftw lib with --enable-sse2 and configured the gromacs with cmake .. -DGMX_CPU_ACCELERATION=SSE4.1. I'd like to know if it is ok to use such a combination? yes, for Gromacs the FFTW should always be compiled with SSE2. You can combine that with any -DGMX_CPU_ACCELERATION setting you want, typically the best that is supported on your platform. Best, Carsten Many thanks. Mingjun-- 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] grompp for minimization: note warning
Dear Justin About following warning in grompp using WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) You said You probably have molecules split across PBC in the input coordinate file. here's nothing wrong in that case I mention that I used input coordinate file from folloowing web site http://cmb.bio.uni-goettingen.de/cholmembranes.html. Structures in this website were equilibrated 195 ns. Nonetheless, has my input coordinate file problem? -- 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] Standard errors
Dear all I would like to calculate the standard deviation (as the error bar) for dV/dlanda.xvg file. I used g_analyze command as the following: g_analyze -ffree_bi_0.9.xvg -av average_0.9 I got: set average *standard deviation* *std. dev. / sqrt(n-1)*… SS16.053822e+01 3.062230e+01 1.936724e-02… Is the amount of in third (standard deviation) or fourth column (std. dev. / sqrt(n-1) ) better than to use as the standard errors? I want to draw dG/d lambda via lambda and show error bar for free energy. Thanks 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
Re: [gmx-users] grompp for minimization: note warning
On 9/16/13 7:37 AM, shahab shariati wrote: Dear Justin About following warning in grompp using WARNING 1 [file em.mdp]: The sum of the two largest charge group radii (6.940482) is larger than rlist (1.20) You said You probably have molecules split across PBC in the input coordinate file. here's nothing wrong in that case I mention that I used input coordinate file from folloowing web site http://cmb.bio.uni-goettingen.de/cholmembranes.html. Structures in this website were equilibrated 195 ns. Nonetheless, has my input coordinate file problem? I have no idea. What file are you using? Visual inspection will make it very obvious whether or not you have broken molecules. My original guess was exactly that - a guess. Based on the supposed size of the group in question, it seemed that it was probably a common membrane issue. Maybe this is or is not the case. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] grompp for minimization: note warning
On 9/16/13 3:06 AM, shahab shariati wrote: Dear Justin Very thanks for your reply. You said I suspect your Gromacs version is somewhat outdated, as recent versions account for periodicity when making this check. I used 4.5.5 version of gromacs. What version of gromacs is more appropriate for my case. When in doubt, always upgrade to the newest version, which is currently 4.6.3. I can't remember when the issue was fixed. Based on your suggestion, I used -maxwarn option for grompp. Then I used -nt 1 option for mdrun, but this step takes too long and Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is larger than the 1-4 table size 2.200 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size step 23: Water molecule starting at atom 10613 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 2122 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.4310875e+05 Maximum force = 2.7179752e+04 on atom 5271 Norm of force = 4.0253470e+02 In this case, it is pretty clear that there is actually something wrong with the input coordinates. -- my em.mdp file is as follows: integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions -- gro, edr, trr and lof file were created. I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp file, but result are the same. Increasing emstep does not make sense. If anything, you should be decreasing it to try to take smaller steps and resolve clashes. In any case, the output tells you where the maximum force is. Fire up your favorite visualization software, look at that atom and the things around it, and figure out what is going on. Is this minimization completely true? Can I use created gro file of this minimization for next step (equilibration)? No, the forces are far too high to be useful. Anything you do will simply crash. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: grompp for minimization: note warning
On 9/16/13 9:47 AM, shahab shariati wrote: Dear Justin My input coordinate file is a gro file (sys.gro). When I visualize that by VMD, all things is ok and true. After minimization, I obtained a gro file (em.gro). When I visualize that by VMD, About 5 DOPC molecules leave bilayer structure and 1 DOPC molecule not only leaves bilayer structure, but also some bonds were broken (there is a broken molecule). Before, I mentioned that my input coordinate file (em.gro) is obtained from reliable website. How to resolve this issue? I attached 2 gro file (sys.gro and em.gro). Resolvation of this issue is very critical and important for me. Please guide me about that. Excuse me for sending this e-mail to personal address. I have to send 2 gro files to you. The proper protocol is to upload the files somewhere publicly accessible and post a download link. I generally do not like large, unrequested attachments. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. As for the charge group error from grompp, I still can see no reason for it. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. Please guide me to resolve these issues. Best wishes -- 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] Re: grompp for minimization: note warning
On 9/16/13 10:52 AM, shahab shariati wrote: Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? I have no idea. I don't know how the box was set or why it was set in that way. It's certainly wrong, but it may not solve the underlying issue. Visualize the area around the drug - there is severe atomic overlap between the lipids and the drug molecule. Clearly it was not built in a manner that will be stable. As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. As I said, I don't know. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: grompp for minimization: note warning
Dear Justin Very very thanks for your quick reply. The sys.gro file is positioned within a box that is too large, a fact that is easily observable in VMD. I suspect that the void space results in instability. If I positioned system in a smaller box, my problem (instability) solved ??? As for the charge group error from grompp, I still can see no reason for it. In the first e-mail, I put charge groups, as you seen, they were ok and true. Thus what is reason of charge group error from grompp. Please guide me to resolve these issues. Best wishes -- 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] Cross compiling GROMACS 4.6.3 for native Xeon Phi, thread-mpi problem
Hi, I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation within the single Xeon Phi. I followed these instructions from Intel for cross compiling for Xeon Phi with cmake: http://software.intel.com/en-us/articles/cross-compilation-for-intel-xeon-phi-coprocessor-with-cmake which includes setting: export CC=icc export CXX=icpc export FC=ifort export CFLAGS=-mmic export CXXFLAGS=$CFLAGS export FFLAGS=$CFLAGS export MPI_C=mpiicc export MPI_CXX=mpiicpc I then run cmake with: cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_FFT_LIBRARY=mkl -DGMX_CPU_ACCELERATION=None -DCMAKE_INSTALL_PREFIX=~/gromacs Note -DGMX_THREAD_MPI=OFF. That seems to work fine (see attached cmake_output.txt), particularly, it finds the MIC Intel MPI: -- Found MPI_C: /opt/intel/impi/4.1.1.036/mic/lib/libmpigf.so;/opt/intel/impi/4.1.1.036/mic/lib/libmpi.so;/opt/i ntel/impi/4.1.1.036/mic/lib/libmpigi.a;/usr/lib64/libdl.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes When I run make everything trundles along fine until: [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o /tmp/iccQqtl2Vas_.s: Assembler messages: /tmp/iccQqtl2Vas_.s:1773: Error: `sfence' is not supported on `k1om' make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 Why is it still building thread_mpi given the -DGMX_THREAD_MPI=OFF at the cmake invocation above? Any suggestions how best to work around this? Thanks, Paul. cmake_output.txt http://gromacs.5086.x6.nabble.com/file/n5011212/cmake_output.txt -- View this message in context: http://gromacs.5086.x6.nabble.com/Cross-compiling-GROMACS-4-6-3-for-native-Xeon-Phi-thread-mpi-problem-tp5011212.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] Help g_energy
Hello. I was calculating the viscosity of hexane through the Gromacs command g_energy. Three files are generated: visco.xvg, evisco.xvg and eviscoi.xvg. The file visco.xvg presents the shear viscosity and bulk, but the value does not match the experimental. I used 8 ns simulation at equilibrium. However, the file evisco.xvg has a value very close to the experimental but has only a time of 2 ns (version 4.0.7). I want to know what is present in the file eviscoi.xvg. Thank you. http://help-gromacs.blogspot.com.br/2013/09/viscosidade-gromacs-407.html -- 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] TPI Results differ in v4.5.7 and v4.6.1
I am sorry for the late follow-up on this subject. My results using PME electrostatics do not show any differences between versions 4.5.4 and 4.6.3 (I also checked with 4.6.1 and it gave the same results): https://www.dropbox.com/s/o2kswrw5eq8fcsp/plot_batch-1_pme.png I hope that you, Niels, have found a solution to your problem, which probably has a different origin from what I initially thought... Best, João On Mon, Jul 1, 2013 at 1:29 PM, João M. Damas jmda...@itqb.unl.pt wrote: I have run TPI using three versions (4.0.4, 4.5.4 and 4.6.1) and three different insertions particles: CH4 (uncharged), Cl- (negative) and Na+ (positive). All TPI were run on the same simulations of SPC water and the three particles taken from GROMOS force-field. Reaction-field was used for electrostatics. https://www.dropbox.com/s/in66zx8t2mrprgt/plot_batch-1.png As you can see, for an uncharged particle all the versions provide the same result. The same does not happen when charged particles are inserted, which hint on problems with the electrostatics between 4.0.4 and 4.[56].X. Like when Niels reported for the Cut-off scheme, the reaction-field provides the same results for 4.5.4 and 4.6.1. Is it indeed a problem with PME? I still have not tested PME, but I think Niels' test foretells the results I'm going to get. Niels, can you confirm this issue is only happening with charged particles? And are you going to file an issue like Szilárd suggested? Best, João On Sat, Jun 29, 2013 at 5:21 PM, João M. Damas jmda...@itqb.unl.ptwrote: Niels, Which force-field did you use? I guess an uncharged CH4 shouldn't be giving different results for TPI when changing coulomb... Actually, coulomb is turned off if there's no charge in the particles to insert, if I remember the code correctly. João On Mon, Jun 24, 2013 at 3:40 PM, Niels Müller u...@nielsm.de wrote: Hi João, Indeed your instinct seems to be good! When switching the Coulomb-Type to Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5. Apparently its an issue with the PME sum. We will investigate further. Am 24.06.2013 um 14:42 schrieb João M. Damas jmda...@itqb.unl.pt: Niels, This is very interesting. At our group, a colleague of mine and I have also identified differences in the TPI integrator between 4.0.X and 4.5.X, but we still haven't had the time to report it properly, since we are using a slightly modified version of the TPI algorithm. Instinctively, we were attributing it to some different behaviours in the RF that are observed between those versions. We also know that the TPI algorithm began allowing PME treatment from 4.5.X onwards, so maybe there are some differences going on the electrostatics level? But, IIRC, no modifications to the TPI code were on the release notes from 4.5.X to 4.6.X... We'll try to find some time to report our findings as soon as possible. Maybe they are related. Best, João On Mon, Jun 24, 2013 at 10:19 AM, Niels Müller u...@nielsm.de wrote: Hi GMX Users, We are computing the chemical potential of different gas molecules in a polymer melt with the tpi integrator. The computations are done for CO2 and CH4. The previous computations were done with v4.5.5 or 4.5.7 and gave equal results. I recently switched to gromacs version 4.6.1, and the chemical potential computed by this version is shifted by a nearly constant factor, which is different for the two gas molecules. We are perplexed what causes this shift. Was there any change in the new version that affects the tpi integration? I will provide the mdp file we used below. The tpi integration is run on basis of the last 10 ns of a 30 ns NVT simulation with 'mdrun -rerun'. Best regards, Niels. # The mdp file: # ; VARIOUS PREPROCESSING OPTIONS cpp = cpp include= define = ; RUN CONTROL PARAMETERS integrator = tpi ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0.5 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible
Re: [gmx-users] Regarding g_sgangle index file
Hello, On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy venkat...@gmail.com wrote: I found g_sgangle is the suitable tool to calculate the angle between two cholesterol rings. But the problem is, I want to do this analysis for my whole system, which has 40 cholesterol molecules. Whereas I can input either two or three atoms in the g_sgangle index file. A quick surf through the gmx-archive yielded a suggestion like: An index group should contain all (1,2) pairs such that the overall group size is a multiple of two. The index group has to be in a particular order, like 1 2 1 2 etc., clip I got the output index file in the same order.,i.e., R5 R0 R5 R0etc. But when I execute g_sgangle, it is saying something wrong with the index file. How to solve this error? How to organize the index file in a multiple of 2? It is only possible to calculate a single angle in one invocation of g_sgangle. You could script your calculation to run g_sgangle once for each of your molecules, but that gets somewhat tedious. With the development version (from the git master branch), you can use a much more powerful 'gmx gangle' tool, which can calculate multiple angles in one go. As an added bonus, you don't need to invoke g_select separately, but can simply provide the selection to the tool. Best regards, Teemu -- 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] Cross compiling GROMACS 4.6.3 for native Xeon Phi, thread-mpi problem
On Mon, Sep 16, 2013 at 7:04 PM, PaulC paul.cah...@uk.fujitsu.com wrote: Hi, I'm attempting to build GROMACS 4.6.3 to run entirely within a single Xeon Phi (i.e. native) with either/both Intel MPI/OpenMP for parallelisation within the single Xeon Phi. I followed these instructions from Intel for cross compiling for Xeon Phi with cmake: http://software.intel.com/en-us/articles/cross-compilation-for-intel-xeon-phi-coprocessor-with-cmake which includes setting: export CC=icc export CXX=icpc export FC=ifort export CFLAGS=-mmic export CXXFLAGS=$CFLAGS export FFLAGS=$CFLAGS export MPI_C=mpiicc export MPI_CXX=mpiicpc I then run cmake with: cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_FFT_LIBRARY=mkl -DGMX_CPU_ACCELERATION=None -DCMAKE_INSTALL_PREFIX=~/gromacs Note -DGMX_THREAD_MPI=OFF. That seems to work fine (see attached cmake_output.txt), particularly, it finds the MIC Intel MPI: -- Found MPI_C: /opt/intel/impi/4.1.1.036/mic/lib/libmpigf.so;/opt/intel/impi/4.1.1.036/mic/lib/libmpi.so;/opt/i ntel/impi/4.1.1.036/mic/lib/libmpigi.a;/usr/lib64/libdl.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes When I run make everything trundles along fine until: [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/errhandler.c.o [ 20%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/tmpi_malloc.c.o [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/atomic.c.o [ 22%] Building C object src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o /tmp/iccQqtl2Vas_.s: Assembler messages: /tmp/iccQqtl2Vas_.s:1773: Error: `sfence' is not supported on `k1om' make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/thread_mpi/pthreads.c.o] Error 1 make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 Why is it still building thread_mpi given the -DGMX_THREAD_MPI=OFF at the cmake invocation above? Because these days thread-MPI not only provides a threading-based MPI implementation for GROMACS, but also some functionality independent from this very feature, namely efficient atomic operations and thread affinity settings. Any suggestions how best to work around this? [ FTFY: Any suggestions how to *fix* this? ] What seems to be causing the trouble here is the atomics support. While x86 normally supports the atomic memory fence operation, Xeon Phi seems to be not so normal and apparently it does not. Now, if you look at src/gmxlib/thread_mpi/pthreads.c:633 you'll see a tMPI_Atomic_memory_barrier() which, for x86, is defined in include/thread_mpi/atomic/gcc_x86.h:105 as #define tMPI_Atomic_memory_barrier() __asm__ __volatile__(sfence; : : : memory) along some other atomic operations for icc among other compilers. What's strange is that the build system checks whether it can compile a dummy C file with the atomics stuff included (see cmake/ThreadMPI.cmake). At first sight it seems that this should fail already at cmake time and should disable the atomics, but apprently it does not. You have two options: - Fix the problem by adding an #elif MACRO_TO_CHECK_FOR_MIC_COMPILATION branch and implement an atomic barrier using the appropriate MIC ASM instruction. - Fix the atomics check such that the lack of atomics support in thread-MPI on MIC is correctly reflected (see cmake/ThreadMPI.cmake:45 which compilescmake/TestAtomics.c). More concretely, the cmake test should fail for MIC build which should result in the disabling of atomics support (and hopefully no compile-time error). I suspect that even the proper fix (first option) may be as simple as a couple of lines worth of changes. Regardless of which option you pick, I would really appreciate if you could upload your fix to gerrit.gromacs.org. You could open an issue on redmine.gromacs.org if you want this issue to be track-able. Cheers, -- Szilárd PS: I hope you know that we have neither SIMD intrinsics support not any reasonable accelerator-aware parallelization for MIC (yet), so don't expect high performance. Thanks, Paul. cmake_output.txt http://gromacs.5086.x6.nabble.com/file/n5011212/cmake_output.txt -- View this message in context: http://gromacs.5086.x6.nabble.com/Cross-compiling-GROMACS-4-6-3-for-native-Xeon-Phi-thread-mpi-problem-tp5011212.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 mailing listgmx-users@gromacs.org
[gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.
This is the command I used pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh And I used OPLS-AA/L all-atom force field.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Seeking-solution-for-the-error-Atom-OXT-in-residue-TRP-323-was-not-found-in-rtp-entry-TRP-with-24-at-tp5011015p5011219.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
Re: [gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.
Hi Santhosh, Try renaming the atom (mind the space): sed 's/OXT/O2 /' pdbfile fixed.pdb And then run pdb2gmx on that. Cheers, Tsjerk On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan santhoshraja...@gmail.com wrote: This is the command I used pdb2gmx -f protein.pdb -o processed.gro -water spce -ignh And I used OPLS-AA/L all-atom force field.. -- View this message in context: http://gromacs.5086.x6.nabble.com/Seeking-solution-for-the-error-Atom-OXT-in-residue-TRP-323-was-not-found-in-rtp-entry-TRP-with-24-at-tp5011015p5011219.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 -- 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] Regarding g_sgangle index file
Thank you sir for the nice tip. I will try it out and let you know if I have any problem. On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola teemu.murt...@gmail.comwrote: Hello, On Sun, Sep 15, 2013 at 5:05 PM, Venkat Reddy venkat...@gmail.com wrote: I found g_sgangle is the suitable tool to calculate the angle between two cholesterol rings. But the problem is, I want to do this analysis for my whole system, which has 40 cholesterol molecules. Whereas I can input either two or three atoms in the g_sgangle index file. A quick surf through the gmx-archive yielded a suggestion like: An index group should contain all (1,2) pairs such that the overall group size is a multiple of two. The index group has to be in a particular order, like 1 2 1 2 etc., clip I got the output index file in the same order.,i.e., R5 R0 R5 R0etc. But when I execute g_sgangle, it is saying something wrong with the index file. How to solve this error? How to organize the index file in a multiple of 2? It is only possible to calculate a single angle in one invocation of g_sgangle. You could script your calculation to run g_sgangle once for each of your molecules, but that gets somewhat tedious. With the development version (from the git master branch), you can use a much more powerful 'gmx gangle' tool, which can calculate multiple angles in one go. As an added bonus, you don't need to invoke g_select separately, but can simply provide the selection to the tool. Best regards, Teemu -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
