[gmx-users] normal mode analysis - regd
Dear Gromacs users, I am performing normal mode analysis (NMA) for a crystal, but in the vibrational spectrum that obtained from NMA, there are no low frequency lattice modes ( i.e., no peaks in spectrum below 50 cm-1). But the spectrum that have obtained from velocity auto correlation function (VACF) contains these low frequency peaks. Here my doubt is why NMA was unable to capture these low frequency peaks(modes) ? Can anybody please help me in this regard. Thank you in advance. Best, Ramesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Special bond between metallic layers protein
Ah, I have to write down the old residue instead of leaving the spaces blank! Like this for a toy pdb file with only 2 platinum atoms it work ;) meaning that the matrix of the distances between all the special atoms is constructed, the special atom around the cut-off distance are linked and no error message is generated ;) But if now I load the true pdb file with 1650 platinum atoms, the distance matrix is again generated *;)* the special atoms around the cut-off distance are again correctly linked *;) *but then I get the following error messages: Making bonds... WARNING: WARNING: Atom 8�%H�%� is used in an interaction of type special bond in the topology database, but an atom of that name was not found in residue number 130. WARNING: WARNING: Atom ��%��%� is used in an interaction of type special bond in the topology database, but an atom of that name was not found in residue number 680. --- Program pdb2gmx, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/pdb2top.c, line: 737 Fatal error: Trying to make impossible special bond (8�%H�%�-��%��%�)! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Nicola Staffolani PhD Biophysics Nanoscience Centre CNISM http://www.unitus.it/biophysics Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cannot write trajectory frame; maybe you are out of disk space
Dear Mark I corrected file permission in my system using chmod -R 777 . But I encountered the same error: File input/output error: Cannot write trajectory frame; maybe you are out of disk space. Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] make install creating infinite recursive directories
BSD Hi All, I am trying to build 4.6.5 for testing, on a Rocks 5.3 cluster (yes it needs upgrading!). I am using one of the compute nodes to do the compiling, using the following: CMAKE_PREFIX_PATH=/share/apps/fftw-3.3.2 /share/apps/cmake-2.8.12.2/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs-4.6.5/ -DGMX_CPU_ACCELERATION=SSE2 This step is fine, as is the make step. But when I type make install, it starts to copy the files to the correct place, but under share it starts to make many recursive gromacs subdirectories. Here is an example early on in the process Installing: /share/apps/gromacs-4.6.5/share/gromacs/./gromacs/top/amber96.ff/rna.r2b As the install proceeds, the number of gromacs/./gromacs/gromacs/gromacs.. directories keeps growing (as in the recursion level keeps going up). Any advice? Thanks Harry Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenbl...@weizmann.ac.il Weizmann Institute of SciencePhone: 972-8-934-3625 234 Herzl St.Facsimile: 972-8-934-4159 Rehovot, 76100 Israel -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Com pulling in reverse Z direction in SMD simulation..
On 4/24/14, 5:21 AM, Kalyanashis wrote: Dear all, I am doing SMD simulation of a enzyme system and I have given the pull option in Z direction. The com pulling options are given below, ;COM pulling pull = umbrella pull_geometry= distance pull_dim = N N Y pull_r1 = 1 pull_r0 = 1 ;pull_constr_tot = 1e-6 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 ;name of reference group pull_group0 = Protein ;pull_weights = 0 ;name of pull group pull_group1 = UNK ;pull_weights = 0 pull_vec1= 0.0 0.0 -1 ;ref. distance at t=0 ;pull_init1 = -2.4477384 -1.0229216 -1.5900776 ;rate of change of ref. gr. [nm/ps] pull_rate1 = 0.0005 ;force constant [KJ mol^-1 nm^-2] pull_k1 = 1586.747 ;pull_kB1= Please kindly tell me, how can I do the same calculation in reverse Z direction?? Change the sign of the pulling vector. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QM/MM simulations
Dear Justin! I'm very sorry to waste your time, but I've got an issue with ORCA support in GROMACS and hope you can help me. I'm installing gromacs-4.6.5 on my Dell PowerEdge R720 machine running Suse 12.3 x64 ( 3.7.10-1.28-desktop core). Installed version of ORCA is orca_3_0_0_linux_x86-64. 0)Previos steps according to the installation guide http://www.gromacs.org/Documentation/Installation_Instructions . 1) cmake /*cmake .. -DGMX_MPI=ON -DGMX_QMMM_PROGRAM=ORCA -DCMAKE_INSTALL_PREFIX=/opt/GROMACS-ORCA/ -DGMX_DOUBLE=on -DFFTW_LIBRARY=/usr/lib64/libfftw3.so.3*/ I get following output. CMake-output.txt http://gromacs.5086.x6.nabble.com/file/n5016041/CMake-output.txt Contents of CMakeCache file is here. CMakeCache.txt http://gromacs.5086.x6.nabble.com/file/n5016041/CMakeCache.txt The GMX_QMMM_PROGRAM variable is properly set in CMakeCache.txt: /*# grep GMX_QMMM_PROGRAM CMakeCache.txt * GMX_QMMM_PROGRAM:STRING=ORCA //ADVANCED property for variable: GMX_QMMM_PROGRAM GMX_QMMM_PROGRAM-ADVANCED:INTERNAL=0/ and in src/config.h /*# grep #define GMX_QMMM_ORCA src/config.h * #define GMX_QMMM_ORCA/ 2) make make install, everything without errors. 3) I create .mdp-file with following QMMM parameters /QMMM = yes QMMM-grps= QMatoms QMmethod = RHF QMbasis = 3-21G QMMMscheme = normal QMcharge = 0 QMmult = 1/ and .ORCAINFO file (as stated in ORCA manual) /# Optimization step in the Lennard-Jones and point charges field of the MM atoms ! QMMMOpt # file containing the Lennard Jones coefficients for the Lennard-Jones interaction #%LJCoefficients temp.LJ # file containing the point charges for the electrostatic interaction #%pointcharges temp.pc %geom # calculate the exact Hessian before the first optimization step Calc_Hess true # in case of a TS optimization the updated Hessian of the previous # TS optimization run is read instead of calculating a new one read_temp_Hess true end/ Variables are set as follows: $BASENAME=topol (name of .tpr and .ORCAINFO files) and $ORCA_PATH=/opt/orca_3_0_0_linux_x86-64 I run //*opt/GROMACS-ORCA/bin/mdrun_mpi_d -v*/ and get /... Back Off! I just backed up md.log to ./#md.log.8# Reading file topol.tpr, VERSION 4.6.5 (double precision) Using 1 MPI process QM/MM calculation requested. Layer 0 nr of QM atoms 24 QMlevel: RHF/3-21G --- Program mdrun_mpi_d, VERSION 4.6.5 Source code file: /home/ak87/Downloads/gromacs-4.6.5/src/mdlib/qmmm.c, line: 778 Fatal error: Ab-initio calculation only supported with Gamess, Gaussian or ORCA. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Halting program mdrun_mpi_d -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. --/ It is quite strange since such problem was noted in earlier versions of GROMACS and have been solved by your patch. Therefore, it should not arise in version 4.6.5, particularly because all variables connected to ORCA are properly defined in Cmake config files. Hope for hearing from you. Thanks in advance! Sincerely yours, Andrey. -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p5016041.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QM/MM simulations
Thanks for rapid answer! I'm willing to try the latest version with your patch. But since I'm quite new to Linux, I'll be very thankful if you explain me how to use gromacs git server, and apply patches. (where to download the source code and the patch) Sincerely, Andrey. -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p5016047.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] QM/MM simulations
On 4/24/14, 12:28 PM, Iamkaant wrote: Thanks for rapid answer! I'm willing to try the latest version with your patch. But since I'm quite new to Linux, I'll be very thankful if you explain me how to use gromacs git server, and apply patches. (where to download the source code and the patch) http://www.gromacs.org/Developer_Zone/Git#Checking_out_the_Gromacs_source_code_using_git Then use the magic copy-paste command that Gerrit gives you (the Download box in checkout mode) on https://gerrit.gromacs.org/#/c/3395/ to apply the patch. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] skipping the EM, NPT and NVT for re-run
Please keep the discussion on the mailing list. On 4/24/14, 4:29 PM, Saman Shahriyari wrote: you mean i should expect a different trajectory every time i do the simulation under the same conditions?! It's certainly possible. http://www.gromacs.org/Documentation/Terminology/Reproducibility One of the many reasons why a single trajectory is often insufficient to make substantive claims. -Justin On Wednesday, April 23, 2014 4:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/23/14, 2:04 AM, Saman Shahriyari wrote: dear users i have an old simulation witch is not working properly. is there anyway i can re-run the simulation using the before md .tpr file, the .gro file and the current .xtc? If you have the .tpr file, that's all you need. You can just re-run it and produce a new .xtc file, though of course there is no guarantee that it will be identical to the original one. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] High Pressure with Martini system
Dear colleagues, I ran an NVT equilibration of a 24mi CG Martini atoms and detected the formation of vacuum spots on the solvent. However, the log file shows a very large negative pressure (about -4e+28) all the time, since the beginning. Despite the negative pressure, when I turn pressure coupling ON, the very first step causes the box to expand (!) too much and then the simulation crashes. Things I tried, and failed: changed the tau_p to several values (1 to 500); changed the compressibility; changed the ref_p from 1 to values closer to the starting pressure; changed time-step from 0.02 up to 0.0005. Additional info: used the insane.py script to solvate the box with polarizable water; there's a large (frozen) bilayer at the center of the box, It, however is smaller than the box sides, to it doesn't interact with itself via PBC. I'm sure I could provide more info, so please ask me for the specifics and I'll reply. Thanks, Ricardo. --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
