[gmx-users] membrane simulations
I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has to move. Can you please suggest me how can I solve this 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
Re: [gmx-users] GROMACS 4.6.3 Static Linking
Hi Vitaly, Impossible just for v4.6.3? It was certainly possible to create static executables for a Cray XE using v4.6.1 (I know, because I have done it). I followed the same procedure for 4.6.3 and have only managed to get dynamic executables (which do not work) hence my question. I will have more of a dig into the build procedure but just wondered if anyone was aware of anything that has changed between these two minor versions (probably in the build process) that could have precipitated this change in behaviour. Cheers Andy Quoting Dr. Vitaly Chaban vvcha...@gmail.com on Sat, 20 Jul 2013 09:42:41 +0200: Soneone said here that static versions are impossible for Cray... Dr. Vitaly V. Chaban On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/**support/documentation/** software/gromacs/compiling_4-**6-1_phase3.phphttp://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-**phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/**libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.**so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.**so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.**so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.**so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_**threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_**threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_**47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_**gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/**libxpmem.so.0 (0x7f50d52c9000) libdmapp.so.1 = /opt/cray/dmapp/default/lib64/**libdmapp.so.1 (0x7f50d5092000) libugni.so.0 = /opt/cray/ugni/default/lib64/**libugni.so.0 (0x7f50d4e72000) libpmi.so.0 = /opt/cray/pmi/default/lib64/**libpmi.so.0 (0x7f50d4c51000) libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0 (0x7f50d4a4e000) libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0 (0x7f50d4849000) libudreg.so.0 = /opt/cray/udreg/default/lib64/**libudreg.so.0 (0x7f50d4641000) libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1 (0x7f50d4432000) libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000) libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1 (0x7f50d3ebd000) /lib/ld64.so.1 = /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000) libquadmath.so.0 = /opt/gcc/4.7.2/snos/lib64/**libquadmath.so.0 (0x7f50d3c87000) libcray_memcpy.so.0 = /opt/cray/lib64/libcray_**memcpy.so.0 (0x7f50d3a84000) libopa.so.1 = /opt/cray/lib64/libopa.so.1 (0x7f50d3882000) librca.so.0 = /opt/cray/rca/default/lib64/**librca.so.0 (0x7f50d367d000) libdl.so.2 = /lib64/libdl.so.2 (0x7f50d3479000) Any ideas? Andy ==**=== Dr Andrew R. Turner e: a.tur...@epcc.ed.ac.uk skype: aturner-epcc t: +44 (0)131 651 3578 p: EPCC, University of Edinburgh EH9 3JZ ==**=== -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- 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/**
Re: [gmx-users] Getting a .tpr file for C-alpha atoms from an all atom .tpr file
Thanks a lot. On Tue, Jul 23, 2013 at 9:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/23/13 11:58 AM, bipin singh wrote: Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. tpbconv -h, particularly point 3. -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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- *--- Thanks and Regards, Bipin Singh* -- 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] Fábio Filippi Matioli Unsubscribe
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[gmx-users] In g_dos, how to calculate the DoS of a certain group in system?
Dear All, I am trying to use g_dos to calculate the DoS of a bio-water system. However, I could not choose a certain group (e.g. the protein) from the index file. My command is like this : g_dos -f x.trr -s x.tpr -n x.ndx And, I also have tried to calculate the DoS of the protein individually from a gas-phase simulation trajectory. But there are some errors like this: --- Program g_dos, VERSION 4.5.5 Source code file: gmx_fft_mkl.c, line: 218 Fatal error: Error initializing Intel MKL FFT; status=2 Could anyone help me? Any suggestion is welcome! Thank you in advance! Wade-- 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] Calculate interaction energy dynamically
Please find below the gmxcheck output. Opposite to what I said earlier it does contain warning messages. Thanks a lot for any suggestion. gmxcheck output: Option Filename Type Description -f /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_r1_ordered.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt -f2 traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -s1 top1.tpr Input, Opt. Run input file: tpr tpb tpa -s2 top2.tpr Input, Opt. Run input file: tpr tpb tpa -c inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -e dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Input, Opt! Energy file -e2 ener2.edr Input, Opt. Energy file -n inp/analysis/dppc_dupc_chol_034x051x015_295K_r1_ordered.ndx Input, Opt! Index file -mdoc.tex Output, Opt. LaTeX file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -vdwfac real 0.8 Fraction of sum of VdW radii used as warning cutoff -bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms -bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms -[no]rmsdbool no Print RMSD for x, v and f -tol real 0.001 Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) -abstol real 0.001 Absolute tolerance, useful when sums are close to zero. -[no]ab bool no Compare the A and B topology from one file -lastenerstring Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 30704 Reading frame 1 time 1000.000 Reading frame 2 time 2000.000 Reading frame 3 time 3000.000 ... Reading frame 12000 time 1200.000 Last frame 12000 time 1200.000 Item#frames Timestep (ps) Step 120011000 Time 120011000 Lambda 120011000 Coords 120011000 Velocities 0 Forces 0 Box 120011000 Checking energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Opened dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr as single precision energy file 68 groups in energy file Reading energy frame 0 time0.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=0. Trying to skip frame expect a crash though frame: -1 (index 0), t: 0.000 Reading energy frame 1 time 1000.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1000. Trying to skip frame expect a crash though Reading energy frame 2 time 2000.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=2000. Trying to skip frame expect a crash though ... WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1.1998e+07. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1.1999e+07. Trying to skip frame expect a crash though Reading energy frame 12000 time 1200.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1.2e+07. Trying to skip frame expect a crash though Last energy frame read 12000 time 1200.000 Found 12001 frames with a timestep of 1000 ps. Checking coordinate file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr, VERSION 4.5.1 (single precision) Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr, VERSION 4.5.1 (single precision) 30704 atoms in file coordinates found box found velocities found Kinetic energy: 112959 (kJ/mol) Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2, the velocities correspond to a temperature of the
R: Re: [gmx-users] Rotation Constraints - PMF + rerun
Dear Carsten, Thank you very much for your very useful help! I'm making some tries to test the orire options that probably will solve my problem. In order to do not waste resource, I thought using the rerun option of mdrun I can use the trajectories generated before, where my mistake was to allow the rotation of my structure. So I generated a new topol.tpr file changing the orire options in the mdp and I made: 1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr 2. trjcat -f traj.trr -o trajout.xtc but in the trajout.xtc there is only one point as I can check for example with: 3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx Could you confirm me that it is not possible follow this idea? In fact I suppose that this method it is not applicable; but it is necessary to generate a new trajectory, because the angular restraints modify completely the trajectory. Or, just to be sure, did I not made the things in the right way? Thank you very much! Anna Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Limitations of simulations?
On 2013-07-24 01:57, Jonathan Saboury wrote: I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? Yes, there are some examples. A paper was published by Shaw and co-worker in J. Amer. Chem. Soc. a year or two ago. I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- 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] Rotation Constraints - PMF + rerun
On Jul 24, 2013, at 12:30 PM, battis...@libero.it wrote: Dear Carsten, Thank you very much for your very useful help! I'm making some tries to test the orire options that probably will solve my problem. In order to do not waste resource, I thought using the rerun option of mdrun I can use the trajectories generated before, where my mistake was to allow the rotation of my structure. So I generated a new topol.tpr file changing the orire options in the mdp and I made: 1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr 2. trjcat -f traj.trr -o trajout.xtc but in the trajout.xtc there is only one point as I can check for example Hm, I am not sure, maybe you need to use -x trj.xtc instead of -o trj.trr to trigger output of all .xtc frames. How many frames are in ../traj.xtc? Carsten with: 3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx Could you confirm me that it is not possible follow this idea? In fact I suppose that this method it is not applicable; but it is necessary to generate a new trajectory, because the angular restraints modify completely the trajectory. Or, just to be sure, did I not made the things in the right way? Thank you very much! Anna Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Limitations of simulations?
On 7/24/13 6:44 AM, David van der Spoel wrote: On 2013-07-24 01:57, Jonathan Saboury wrote: I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? Yes, there are some examples. A paper was published by Shaw and co-worker in J. Amer. Chem. Soc. a year or two ago. I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! For the rest of us mere mortals who don't have access to specialized hardware that allows for 10- or 20-microsecond simulations, the brute force approach is rather futile. Techniques like steered MD and Hamiltonian replica exchange MD are probably more feasible. Unbiased simulations of sufficient length, using standard supercomputing hardware, would probably take years. -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] Calculate interaction energy dynamically
On 7/24/13 5:49 AM, Davit Hakobyan wrote: Please find below the gmxcheck output. Opposite to what I said earlier it does contain warning messages. Thanks a lot for any suggestion. gmxcheck output: Option Filename Type Description -f /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_r1_ordered.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt -f2 traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -s1 top1.tpr Input, Opt. Run input file: tpr tpb tpa -s2 top2.tpr Input, Opt. Run input file: tpr tpb tpa -c inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -e dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Input, Opt! Energy file -e2 ener2.edr Input, Opt. Energy file -n inp/analysis/dppc_dupc_chol_034x051x015_295K_r1_ordered.ndx Input, Opt! Index file -mdoc.tex Output, Opt. LaTeX file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -vdwfac real 0.8 Fraction of sum of VdW radii used as warning cutoff -bonlo real 0.4 Min. fract. of sum of VdW radii for bonded atoms -bonhi real 0.7 Max. fract. of sum of VdW radii for bonded atoms -[no]rmsdbool no Print RMSD for x, v and f -tol real 0.001 Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) -abstol real 0.001 Absolute tolerance, useful when sums are close to zero. -[no]ab bool no Compare the A and B topology from one file -lastenerstring Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 30704 Reading frame 1 time 1000.000 Reading frame 2 time 2000.000 Reading frame 3 time 3000.000 ... Reading frame 12000 time 1200.000 Last frame 12000 time 1200.000 Item#frames Timestep (ps) Step 120011000 Time 120011000 Lambda 120011000 Coords 120011000 Velocities 0 Forces 0 Box 120011000 Checking energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Opened dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr as single precision energy file 68 groups in energy file Reading energy frame 0 time0.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=0. Trying to skip frame expect a crash though frame: -1 (index 0), t: 0.000 Reading energy frame 1 time 1000.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1000. Trying to skip frame expect a crash though Reading energy frame 2 time 2000.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=2000. Trying to skip frame expect a crash though ... WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1.1998e+07. Trying to skip frame expect a crash though WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1.1999e+07. Trying to skip frame expect a crash though Reading energy frame 12000 time 1200.000 WARNING: there may be something wrong with energy file dat/enr/dppc_dupc_chol_034x051x015_295K_r1_ordered.edr Found: step=-1, nre=68, nblock=0, time=1.2e+07. Trying to skip frame expect a crash though Last energy frame read 12000 time 1200.000 This is smelling a bit buggy to me, but then too, I've never tried a rerun on a reordered trajectory. As a test, can you produce an .edr file from a rerun of the original trajectory (i.e. not manipulated by trjorder)? -Justin Found 12001 frames with a timestep of 1000 ps. Checking coordinate file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr, VERSION 4.5.1 (single precision) Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K_r1_ordered.tpr, VERSION 4.5.1 (single precision) 30704
Re: [gmx-users] membrane simulations
On 7/24/13 2:55 AM, Sathish Kumar wrote: I am doing simulation of metal clusters with membranes by position restrain (with f=1000) the membrane. In this simulation the structure of metal cluster is collapsed after entering into membrane. I want to preserves its structure with out doing position restrain the metal cluster because it has to move. Can you please suggest me how can I solve this problem. Geometry is a function of the topology. Setting correct parameters for whatever the desired or expected geometry is should alleviate the issue. -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] interaction energy using g_enemat
Dear All, I want to calculate interaction energy per residue. Below is the command i used: g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm my groups.dat file contains these lines: 3 strand1_SER_34 strand1_THR_36 strand1_TYR_37 When i execute the above g_enemat command i get the below error message: WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36 (34,36)in energy file WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37 (34,37)in energy file My strand.edr file looks like this: LJ-SR:strand1_SER_34-strand1_THR_36 Coul-SR:strand1_SER_34-strand1_TYR_37 Please can I get some suggestions on how to get around this problem. Kind Regards, Chetan Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt Das Forschungszentrum oeffnet seine Tueren am Sonntag, 29. September, von 10:00 bis 17:00 Uhr: http://www.tagderneugier.de -- 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
R: Re: [gmx-users] Rotation Constraints - PMF + rerun
in my traj.xtc file there are 1 frame every 10 ps from 0 ps to 1 ps, therefore in total 1001 frames. I tried -x trj.xtc instead -o trj.trr, but mdrun has generated a file trj.xtc. trr Many thanks! Anna Messaggio originale Da: ckut...@gwdg.de Data: 24/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF + rerun On Jul 24, 2013, at 12:30 PM, battis...@libero.it wrote: Dear Carsten, Thank you very much for your very useful help! I'm making some tries to test the orire options that probably will solve my problem. In order to do not waste resource, I thought using the rerun option of mdrun I can use the trajectories generated before, where my mistake was to allow the rotation of my structure. So I generated a new topol.tpr file changing the orire options in the mdp and I made: 1. mdrun -rerun ../traj.xtc -s topol.tpr -o trj.trr 2. trjcat -f traj.trr -o trajout.xtc but in the trajout.xtc there is only one point as I can check for example Hm, I am not sure, maybe you need to use -x trj.xtc instead of -o trj.trr to trigger output of all .xtc frames. How many frames are in ../traj.xtc? Carsten with: 3. g_gyrate -f trajout.xtc -s topol.tpr -n index.ndx Could you confirm me that it is not possible follow this idea? In fact I suppose that this method it is not applicable; but it is necessary to generate a new trajectory, because the angular restraints modify completely the trajectory. Or, just to be sure, did I not made the things in the right way? Thank you very much! Anna Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post
Re: [gmx-users] OpenSuse 12.1 + CUDA Installation Error
On 24.07.2013 04:08, Carlos Bueno wrote:
*Hi,*
*I keep getting errors when I try to install gromacs in OpenSuse 12.1.*
*I have installed cuda 5.0 and the nvidia cards. **I have tried with
different parameters for cmake:*
How did you install Cuda5? What did you install and how?
I have one OpenSuSE 12.1 box that works as a cluster head
and serves to gpu-clusters. Every software except the
nvidia gpu driver is installed on this box for usage by
the nodes.
Installing a gpu-ready OpenSuSE 12.1 involves (for example, YMMD)
* add community- and extra-repositories through yast/repositories,
these involve (here):
(a) included in yast/repositories (activate only)
Packman Repository
openSUSE BuildService - devel:languages:perl
openSUSE BuildService - devel:languages:python
Education
science
(b) extra (add manually or ba script)
devel:/tools
devel:/libraries:/c_c++
devel:/gcc
you can do the latter by script:
#
#!/bin/sh
Uri[1]=http://download.opensuse.org/repositories/devel:/tools/openSUSE_12.1/;
Name[1]=devel:/tools
Uri[2]=http://download.opensuse.org/repositories/devel:/libraries:/c_c++/openSUSE_12.1/;
Name[2]=devel:/libraries:/c_c++
Uri[3]=http://download.opensuse.org/repositories/devel:/gcc/openSUSE_12.1/;
Name[3]=devel:/gcc
#
for i in 1 2 3; do
zypper --gpg-auto-import-keys ar ${Uri[i]} ${Name[i]}
zypper modifyrepo --refresh ${Name[i]}
done
#
* install gcc 4.6 / g++ 4.6 through yast
* install fftw 3.3.3 through yast, look for the following packages:
gpuclu:~ # rpm -qa |grep fftw
libfftw3-3-3.3.3-5.1.x86_64
fftw3-devel-3.3.3-5.1.x86_64
fftw3-3.3-18.1.3.x86_64
fftw3-threads-3.3-18.1.3.x86_64
fftw3-threads-devel-3.3.3-5.1.x86_64
libfftw3_threads3-3.3.3-5.1.x86_64
* install blas-devel, lapack-devel, gsl-devel through yast
* Important: remove everything Nvidia-related stuff through yast, reboot
* download and install (compile) the gpu driver
NVIDIA-Linux-x86_64-319.32.run
check if it functions properly (after reboot)
* download and install CUDA from Nvidia:
cuda_5.0.35_linux_64_suse12.1-1.run
if everything works, the command
nvidia-smi
should display some meaningful output.
my € 0.05
M.
--
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[gmx-users] Index error
Dear Users, I would like to know if anyone may help me understand how to update the index file. I am trying to simulate a dna in solution. I have relaxed a Solvent with attached min.mdp file without problem. in the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But the index file did not work. I have trying to generate an index file using the file.gro from min.mdp but it doesn't work. Below is the obtained error. Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA_chain_B' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Velocities were taken from a Maxwell distribution at 10 K --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1332 Fatal error: Group NA+SOL referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am looking forward to have any suggestion that might help me in this case. I wish all of you a wonderful day. Collins -- 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] Index error
On 7/24/13 8:34 AM, Collins Nganou wrote: Dear Users, I would like to know if anyone may help me understand how to update the index file. I am trying to simulate a dna in solution. I have relaxed a Solvent with attached min.mdp file without problem. in the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But the index file did not work. I have trying to generate an index file using the file.gro from min.mdp but it doesn't work. It is simple to merge solvent and ion groups. See tutorial material or type 'help' at the make_ndx prompt. We can't help you if we don't know what you did. Below is the obtained error. Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA_chain_B' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Velocities were taken from a Maxwell distribution at 10 K --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1332 Fatal error: Group NA+SOL referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If you use make_ndx, group names will never contain + signs. Merged groups are joined via _ (underscore), but it sounds like you haven't even gotten that far, given the statement above. -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] interaction energy using g_enemat
On 7/24/13 7:47 AM, Poojari, Chetan wrote: Dear All, I want to calculate interaction energy per residue. Below is the command i used: g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm my groups.dat file contains these lines: 3 strand1_SER_34 strand1_THR_36 strand1_TYR_37 When i execute the above g_enemat command i get the below error message: WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36 (34,36)in energy file WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37 (34,37)in energy file My strand.edr file looks like this: LJ-SR:strand1_SER_34-strand1_THR_36 Coul-SR:strand1_SER_34-strand1_TYR_37 Please can I get some suggestions on how to get around this problem. I think g_enemat is buggy. People post the same issue or slight variants of it all the time. My version 4.6 installation fares even worse, as group names aren't even recognized (set to 'null' for everything). You can get interaction energies over time using g_energy, but I don't think g_enemat currently functions properly. -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] Calculate interaction energy dynamically
Thank you again for your time and help. Performing rerun on the original system passes without warnings with the following output: Option Filename Type Description -s inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr InputRun input file: tpr tpb tpa -o /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_testrerun.trr Output Full precision trajectory: trr trj cpt -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c crd/dynmc_end/dppc_dupc_chol_034x051x015_295K_testrerun.gro Output Structure file: gro g96 pdb etc. -e dat/enr/dppc_dupc_chol_034x051x015_295K_testrerun.edr Output Energy file -g out/dppc_dupc_chol_034x051x015_295K_testrerun.log Output Log file -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file -fieldfield.xvg Output, Opt. xvgr/xmgr file -tabletable.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerun /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt -tpitpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -eisam.edi Input, Opt. ED sampling input -eosam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jobam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -nt int0 Number of threads to start (0 is guess) -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-1 Global communication frequency -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]cpnum bool no Keep and number checkpoint files -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names -maxhreal -1 Terminate after 0.99 times this time (hours) -multi int0 Do multiple simulations in parallel -replex int0 Attempt replica exchange every # steps -reseed int-1 Seed for replica exchange, -1 is generate a seed -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr, VERSION 4.5.1 (single precision) Starting 8 threads Making 2D domain decomposition 4 x 2 x 1 WARNING: This run will generate roughly 8779 Mb of data starting md rerun 'DPPC/DUPC/CHOLESTEROL BILAYER', reading coordinates
Re: [gmx-users] Calculate interaction energy dynamically
On 7/24/13 9:25 AM, Davit Hakobyan wrote: Thank you again for your time and help. Performing rerun on the original system passes without warnings with the following output: Option Filename Type Description -s inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr InputRun input file: tpr tpb tpa -o /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_testrerun.trr Output Full precision trajectory: trr trj cpt -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi state.cpt Input, Opt. Checkpoint file -cpo state.cpt Output, Opt. Checkpoint file -c crd/dynmc_end/dppc_dupc_chol_034x051x015_295K_testrerun.gro Output Structure file: gro g96 pdb etc. -e dat/enr/dppc_dupc_chol_034x051x015_295K_testrerun.edr Output Energy file -g out/dppc_dupc_chol_034x051x015_295K_testrerun.log Output Log file -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file -fieldfield.xvg Output, Opt. xvgr/xmgr file -tabletable.xvg Input, Opt. xvgr/xmgr file -tablep tablep.xvg Input, Opt. xvgr/xmgr file -tableb table.xvg Input, Opt. xvgr/xmgr file -rerun /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr Input, Opt! Trajectory: xtc trr trj gro g96 pdb cpt -tpitpi.xvg Output, Opt. xvgr/xmgr file -tpid tpidist.xvg Output, Opt. xvgr/xmgr file -eisam.edi Input, Opt. ED sampling input -eosam.edo Output, Opt. ED sampling output -j wham.gct Input, Opt. General coupling stuff -jobam.gct Output, Opt. General coupling stuff -ffout gct.xvg Output, Opt. xvgr/xmgr file -devout deviatie.xvg Output, Opt. xvgr/xmgr file -runav runaver.xvg Output, Opt. xvgr/xmgr file -px pullx.xvg Output, Opt. xvgr/xmgr file -pf pullf.xvg Output, Opt. xvgr/xmgr file -mtx nm.mtx Output, Opt. Hessian matrix -dn dipole.ndx Output, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -nt int0 Number of threads to start (0 is guess) -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[no]ddcheck bool yes Check for all bonded interactions with DD -rdd real 0 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates -rconreal 0 Maximum distance for P-LINCS (nm), 0 is estimate -dlb enum autoDynamic load balancing (with DD): auto, no or yes -dds real 0.8 Minimum allowed dlb scaling of the DD cell size -gcomint-1 Global communication frequency -[no]v bool no Be loud and noisy -[no]compact bool yes Write a compact log file -[no]seppot bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -pforce real -1 Print all forces larger than this (kJ/mol nm) -[no]reprod bool no Try to avoid optimizations that affect binary reproducibility -cpt real 15 Checkpoint interval (minutes) -[no]cpnum bool no Keep and number checkpoint files -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names -maxhreal -1 Terminate after 0.99 times this time (hours) -multi int0 Do multiple simulations in parallel -replex int0 Attempt replica exchange every # steps -reseed int-1 Seed for replica exchange, -1 is generate a seed -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr, VERSION 4.5.1 (single precision) Starting 8 threads Making 2D domain decomposition 4 x 2 x 1 WARNING: This run will generate roughly 8779 Mb of data starting md
[gmx-users] Umbrella Sampling _ pulled ion
Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let me know how I would be able to define a new group for a specific ion ? Did I make a mistake in defining a new group? Would you please give me any suggestions? Thanks in advance, Sincerely, Shima -- 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] Umbrella Sampling _ pulled ion
On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let me know how I would be able to define a new group for a specific ion ? Did I make a mistake in defining a new group? What you did in terms of index group content is fine. The error message means that the file called index_US.ndx is not present in the working directory, or it has the wrong permissions. -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
R: Re: [gmx-users] Rotation Constraints - PMF - external potential
Dear Carsten could you give me more information about your suggestions? I tried but probably I did not understand well what you meant. In order to avoid the rotation of the structure A and of the structure B, I have defined into the index file a group A_B that contains A+B and I have setted in the mdp file the following parameters: ; Orientation restraints: No or Yes orire= yes ; Orientation restraints force constant and tau for time averaging orire-fc = 500 orire-tau= 100 orire-fitgrp = A_B ; Output frequency for trace(SD) and S to energy file nstorireout = 100 As I have synthetically described in the first post , the structures A and B (characterized by a cylindrical shape) are defined by a number of 32 unit- structures that I call s. Into the itp is defined the topology for the s structure, and so in order to put an orientation restraints between atoms that are not included into the same itp file, I cannot put into the topology a section like that described into the manual 4.6.2 pag. 92 namely, [ orientation_restraints ], could I ? Could you tell me How I can fix the orientation of the systems A and B? I don't understand the manual's explanation about the orire-fitgrp: (fit group for orientation restraining. This group of atoms is used to determine the rotation R of the system with respect to the reference orientation. The reference orientation is the starting conformation of the first subsystem. For a protein, backbone is a reasonable choice) How one have to give the group? using an index file or defining the group in the topology? Thank you very much! Anna Messaggio originale Da: ckut...@gwdg.de Data: 23/07/2013 13.09 A: battis...@libero.itbattis...@libero.it, Discussion list for GROMACS usersgmx-users@gromacs.org Ogg: Re: [gmx-users] Rotation Constraints - PMF Hi Anna, please have a look at the Enforced Rotation Section in the Gromacs 4.6 manual. You can restrain the angle of rotation about an axis by setting the rotation rate to zero. There is also a 4.5 add-on available with rotational restraints in the Gromacs git repository (branch rotation). For more info you may want to look at this page: http://www.mpibpc.mpg.de/grubmueller/rotation Best, Carsten On Jul 23, 2013, at 12:18 PM, battis...@libero.it wrote: Dear user and expert, I'd like ask you a suggestion about a problem that I will try present you schematically. I have got a structure s and I have generated the topolgy file itp for it. A number of separate s in turn generate a complex structure A, that is characterized by a cylindrical shape. Now, I constructed a system with two cylindrical structures, A and B (in total made by 64 s structures), and I'd like make an Umbrella Sampling calculation in order to study the PMF varying the distance between A and B. My problem is that I'd like fix the orientation of the axis of each structure A and B long the z axis, during the dynamics. So I need to put a force into the system or a constrain, such that when the axis of A or B rotates respect to z axis, the force puts back the axis of the structure in the z direction. It this possible? If it is so, could you tell me how to do that? Than you very much, Anna -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Umbrella Sampling _ pulled ion
Yes, Thanks. Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings? To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US? Many many thanks for your time and suggestions. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file: pull_group1 = Ces_ion So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) : [ system] ... [protein] ... [protein-H] ... [ Ces_ion ] 85563 But after running the grompp, I get this fatal error: File input/output error: index_US.ndx Would you please let me know how I would be able to define a new group for a specific ion ? Did I make a mistake in defining a new group? What you did in terms of index group content is fine. The error message means that the file called index_US.ndx is not present in the working directory, or it has the wrong permissions. -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] Box dimension size errors in MARTINI soft core simulation
I am fairly new to gromacs and I am trying to run a thermodynamic integration simulation of a ligand disappearing in a box of octanol at a single set lambda point. I have previous successful nvt and npt runs of this system. When I have added the free energy portions to the input file, I get the following error: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This seems unusual. The box dimensions are 9.45 nm x 9.45 x 9.45 nm so that is fairly large even accounting for some shrinkage with a disappearing ligand. Cutoffs in the input file are set as follows: rlist =1.4, rvdw=1.2, rcoulomb=1.2. Doubling any of them would still be less than 3 nm which is significantly smaller than the box size. Is there anything I am missing or any suggestions that others can give me? Thank you, Scott -- 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] Box dimension size errors in MARTINI soft core simulation
On 7/24/13 4:33 PM, Scott Pendley wrote: I am fairly new to gromacs and I am trying to run a thermodynamic integration simulation of a ligand disappearing in a box of octanol at a single set lambda point. I have previous successful nvt and npt runs of this system. When I have added the free energy portions to the input file, I get the following error: Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This seems unusual. The box dimensions are 9.45 nm x 9.45 x 9.45 nm so that is fairly large even accounting for some shrinkage with a disappearing ligand. The available information suggests the system has become unstable and is imploding. See general troubleshooting information at http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. Cutoffs in the input file are set as follows: rlist =1.4, rvdw=1.2, rcoulomb=1.2. Doubling any of them would still be less than 3 nm which is significantly smaller than the box size. Is there anything I am missing or any suggestions that others can give me? I wouldn't mess with the cutoffs; they're an essential part of the force field. For further diagnostics, please consider the points above and provide your .mdp file and Gromacs version. -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] Limitations of simulations?
For the rest of us mere mortals who don't have access to specialized hardware that allows for 10- or 20-microsecond simulations, the brute force approach is rather futile. Techniques like steered MD and Hamiltonian replica exchange MD are probably more feasible. Unbiased simulations of sufficient length, using standard supercomputing hardware, would probably take years. -Justin Do you think implicit water with 10-20 ligands would be able to do it? I see that the gpu accelerated implicit gets about 100-150 ns/day so a 10-20 day simulation would yield that time frame, no? Thanks :) -- 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] Limitations of simulations?
On 7/24/13 9:16 PM, Jonathan Saboury wrote: For the rest of us mere mortals who don't have access to specialized hardware that allows for 10- or 20-microsecond simulations, the brute force approach is rather futile. Techniques like steered MD and Hamiltonian replica exchange MD are probably more feasible. Unbiased simulations of sufficient length, using standard supercomputing hardware, would probably take years. -Justin Do you think implicit water with 10-20 ligands would be able to do it? I see that the gpu accelerated implicit gets about 100-150 ns/day so a 10-20 day simulation would yield that time frame, no? Thanks :) In an implicit, non-periodic system, it is more likely that the ligand will float away from the protein. I've tried it and that's all that ever happens. Moreover, the current Gromacs version does not support implicit solvent on GPU and the previous version that did had very limited functionality. -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] (no subject)
In an implicit, non-periodic system, it is more likely that the ligand will float away from the protein. I've tried it and that's all that ever happens. Moreover, the current Gromacs version does not support implicit solvent on GPU and the previous version that did had very limited functionality. -Justin Hm, I am probably completely wrong about this, but can you do implicit solvent and Periodic Box Conditions? If so, does it give similar ns/day? Thanks! -- 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] binding energy for membrane system
Hello: I notice that the manual or tutorial in Gromacs (FEP, unbralla sampling, TI and so on) website for binding energy evaluation are all for protein in water. I am just wondering how can we evaluate the protein/ligand binding affinity for membrane system accurately? Probably the most difficult thing is to evaluate the term from protein/lipids and protein/water part, since the system is heterogeneous instead of homogeneous. thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
