Re: [gmx-users] gromacs
Set the installed path and library path of Gromacs in .bashrc file and source it On Tue, Apr 1, 2014 at 1:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.comwrote: i used the pdb2gmx command but i get a message command not found. can you help me -- 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. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- 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] MPI error in gromacs 4.6
Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 318 318; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = berendsen; Berendsen thermostat pcoupltype= isotropic; uniform scaling of box vectors tau_p= 1.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; Velocity generation is on gen_temp= 318; reference temperature, for protein in K Kind regards-- Ankita Naithani -- 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
Re: [gmx-users] MPI error in gromacs 4.6
It might be some typographical errors. Check the mdp file thoroughly. I think semicolon is required for the last line in your mdp file On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi Pavan, Thank you for your response. I am trying to generate the tpr file with the following parameter; ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter file. On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar kumar.pavan...@gmail.com wrote: Hello Ankita You have to just include the following line in your mdp file cutoff-scheme=Verlet And run your grompp with the modfied mdp file to generate tpr file and then mdrun. Hope this doesn't give you the same error On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani ankitanaith...@gmail.comwrote: Hi, I am trying to run a simulation of my protein (monomer ~500 residues). I had few questions and erors regarding the same. I have previously run the simulation of the apo form of the same protein using Gromacs 4.5.5 which was available at the cluster facility I was using and also which is installed in my system. However, when I tried to run the holo form, I got error : Fatal error: 11 particles communicated to PME node 106 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors This I figured out could be solved using a lower timestep as my previous timestep was 4fs and now I have reduced it to 3fs which should work fine now. However, after producing the tpr file for production run in my GROMACS 4.5.5, I realised that the grant for the cluster facility is over and the new clusters which I am trying to set up the same protein for support only gromacs 4.6. I am trying to run the code in these clusters and I get he following error: --- Program mdrun_mpi, VERSION 4.6.3 Source code file: /home/gromacs-4.6.3/src/kernel/runner .c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors - 1. I wanted help with my mdp options to make it compatible. 2. Since my pevious calculations were based on gromacs 4.5.5, switching to gromacs 4.6, would that break the continuity of the run or would that bring about differences in the way the trajectories would be analysed? Below, is my mdp file title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= ; 0.003 * = 10 ps or 100 n dt= 0.003; 3 fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout= 0; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 5 ps nstenergy= 1000; save energies every 5 ps nstlog= 1000; update log file every 5 ps energygrps = Protein ATP ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 25 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) rlistlong= 1.0; long-range neighborlist cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT nstcomm = 10; remove com every 10 steps ; Temperature coupling is on tcoupl= V-rescale
Re: [gmx-users] Adding TPO and SEP to G53a6 Forcefield
...@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. -- Best Pavan Kumar -- 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] Out of Disk Space
Hi everybody, I am running mdrun_mpi V 4.6.5 for nsteps=1000; 20 ns My simulation is getting stopped at 500ps and I am getting following error even though i have enough space on my cluster around 17 GB. *Cannot fsync 'md1.trr'; maybe you are out of disk space?* *Cannot fsync 'md1.log'; maybe you are out of disk space?* I have executed for two times, each time i get different error. What is the reason for the above error. I am sharing my mdp file. Any help is appreciated. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- 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] Guidance on how to install Gromacs-5.0-beta2
Hello Yogendra, Remove -DGMX_BUILD_OWN_FFTW=ON argument and add CMAKE_PREFIX_PATH=/path/to/fftw I hope it works On Fri, Feb 21, 2014 at 4:31 PM, Yogendra Ramtirtha ramtirtha.yogen...@gmail.com wrote: Hello, Actually, I am trying to install Gromacs-5.0-beta2 on my systemwhich has Ubuntu 12.04. Everything went fine untill the make command which gives me the following error - ( [ 0%] Performing download step (verify and extract) for 'fftwBuild' -- verifying file... file='http:/www.fftw.org/fftw-3.3.3.tar.gz' -- verifying file... warning: did not verify file - no URL_HASH specified? -- extracting... src='/home/yogendra/Desktop/gromacs-5.0-beta2/build/src/contrib/fftw/fftwBuild-prefix/src/http:/ www.fftw.org/fftw-3.3.3.tar.gz' dst='/home/yogendra/Desktop/gromacs-5.0-beta2/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild' CMake Error at fftwBuild-stamp/extract-fftwBuild.cmake:11 (message): error: file to extract does not exist: '/home/yogendra/Desktop/gromacs-5.0-beta2/build/src/contrib/fftw/fftwBuild-prefix/src/http:/ www.fftw.org/fftw-3.3.3.tar.gz' make[2]: *** [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-download] Error 1 make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2 make: *** [all] Error 2 ) To deal with this error, I manually installed fftw-3.3.3 on my desktop but the major hurdle now is that I don't know how to proceed with Gromacs installation. Please can anyone guide me, I need help as Gromacs is a part of my academic work. ( I am a graduate student of biotechnology. ) -- 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. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- 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] Fwd: Segmentation fault with mdrun
-- Forwarded message -- From: Pavan Kumar kumar.pavan...@gmail.com Date: Thu, Feb 20, 2014 at 3:34 PM Subject: Segmentation fault with mdrun To: gromacs.org_gmx-users-requ...@maillist.sys.kth.se Hello, I am using gromacs 4.6.5. I am running my code on the cluster providing 8 nodes and 4 processor each. I am getting Segmentation Fault while running mdrunmpi My command *mpirun -n 8 mdrunmpi.4.6.5 -v -deffnm em* More Details: *Machine : GNU/Linux x86_64* *gcc (GCC) 4.3.3 * *cmake version 2.8.3* Compilation Details: *I have compiled my code using mpich compiler * *cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_C_COMPILER=/opt/mpich2/gnu/bin/mpicc -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2 -DCMAKE_INSTALL_PREFIX=/home/garuda/garuda3/gromacs465* If there is any problem in compiling the code itself, what is the error and how it could be corrected. Please give me any solutions, why i am getting the above error. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 -- 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] Segmentation Fault with mdrun_mpi
Hello, I am using gromacs 4.6.5. I am running my code on the cluster providing 8 nodes and 4 processor each. I am getting Segmentation Fault while running mdrunmpi My command *mpirun -n 8 mdrunmpi.4.6.5 -v -deffnm em* More Details: *Machine : GNU/Linux x86_64* *gcc (GCC) 4.3.3* *cmake version 2.8.3* Compilation Details: *I have compiled my code using mpich compiler * *cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON -DCMAKE_C_COMPILER=/opt/mpich2/gnu/bin/mpicc -DGMX_BUILD_OWN_FFTW=ON -DGMX_CPU_ACCELERATION=SSE2 -DCMAKE_INSTALL_PREFIX=/home/garuda/garuda3/gromacs465* mdrun log file is attached. Please find the attachment. If there is any problem in compiling the code itself, what is the error and how it could be corrected. Please give me any solutions, why i am getting the above error. -- Thanks Regards, Pavan Kumar Project Engineer CDAC -KP Ph +91-7676367646 Log file opened on Thu Feb 20 17:52:25 2014 Host: compute-1-21.local pid: 7187 nodeid: 0 nnodes: 8 Gromacs version:VERSION 4.6.5 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE2 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: disabled Built on: Tue Feb 4 14:40:23 IST 2014 Built by: garuda3@compute-1-0.local [CMAKE] Build OS/arch: Linux 2.6.18-53.1.4.el5 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU X5460 @ 3.16GHz Build CPU family: 6 Model: 23 Stepping: 6 Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 sse4.1 ssse3 C compiler: /opt/mpich2/gnu/bin/mpicc GNU gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14) C compiler flags: -msse2-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG :-) G R O M A C S (-: GROtesk MACabre and Sinister :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) ./bin/mdrun_mpi (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = steep nsteps = 500 init-step= 0 cutoff-scheme= Verlet ns_type = Grid nstlist = 1 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx
