[gmx-users] Still having issues analyzing normal-mode hessian
Hello, I have successfully generated a 945MB mtx hessian storing the normal modes of a ~1500AA protein using mdrun with the "nm" integrator and no cutoffs. However, when I try to analyze the normal modes and create trajectories using g_nmeig, I can't seem to generate any output. I am running g_nmeig_mpi_d with the following options: "mpiexec_mpt g_nmeig_mpi_d -f input.mtx -s NMA.tpr -of NMA_freq.xvg -ol NMA_val.xvg -v NMA_vec.trr" and have been letting it run a few times for up to 5 days on 128 Itanium nodes with 120gb maximum memory. When the job finally aborts after running out of cpu time, I get a standard output file that's about 8GB (which I am unable to open). Is there a way to force g_nmeig to generate some output or at least show me what is going on? Am I running it with the correct options? There isn't a lot of documentation on these normal-mode specific programs so I don't know how to begin troubleshooting. Thanks, *Bryan Roessler | Graduate Research Assistant* UAB | The University of Alabama at Birmingham *uab.edu/cmdb* Knowledge that will change your world -- 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] Normal Mode Analysis -- Expected Output
My problem was here: >nsteps = 10 which should read nsteps = 1 I was under the assumption that the step numbers would correspond to the number of calculated eigenvectors. All eigenvectors are calculated in step 1. Thanks, Bryan On Thu, Apr 11, 2013 at 12:33 PM, David van der Spoel wrote: > On 2013-04-11 17:57, Bryan Roessler wrote: > >> Hello, >> >> I am running a normal mode analysis on a ~1500AA protein with the >> following >> mdp parameters: >> >> Log file opened on Tue Apr 9 09:55:00 2013 >> Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 >> Gromacs version:VERSION 4.6.1 >> Precision: double >> Memory model: 64 bit >> MPI library:MPI >> OpenMP support: disabled >> GPU support:disabled >> invsqrt routine:gmx_software_invsqrt(x) >> CPU acceleration: AVX_256 >> FFT library:fftw-3.3.2-sse2 >> Large file support: enabled >> RDTSCP usage: enabled >> Built on: Fri Mar 15 09:20:59 CDT 2013 >> Built by: asndcy@uv [CMAKE] >> Build OS/arch: Linux 3.0.58-0.6.6-default x86_64 >> Build CPU vendor: GenuineIntel >> Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz >> Build CPU family: 6 Model: 45 Stepping: 7 >> Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr >> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 >> sse4.2 ssse3 tdt x2apic >> C compiler: /opt/sgi/mpt/mpt-2.07/bin/**mpicc GNU gcc (GCC) 4.7.2 >> C compiler flags: -mavx -Wextra -Wno-missing-field-**initializers >> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas >> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 >> -DNDEBUG >> >> >> :-) G R O M A C S (-: >> >> Good gRace! Old Maple Actually Chews Slate >> >> :-) VERSION 4.6.1 (-: >> >> 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. >> >> :-) /opt/asn/apps/gromacs_4.6.1/**bin/mdrun_mpi_d (double >> precision) (-: >> >> >> 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 --- >> >> >> Changing rlist from 1.47 to 1.4 for non-bonded
[gmx-users] Re:
Thank you for your response. I am running double precision gromacs and I have minimized my structure down to ~1 Fmax, so neither of those concerns should be a problem. On Thu, Apr 11, 2013 at 12:15 PM, abhijit Kayal wrote: > > in normal mode analysis you will get 3n vibrational degrees of freedom, > where first 6 should have zero frequency. If some of them are negative that > means that you are in saddle point or your structure is not properly > optimized. So for normal mode analysis you have to be very careful that > your structure is properly optimized. So you have to run gromacs in double > precision. > -- > Abhijit kayal > Research Scholar > Theoritical Chemistry > IIT Kanpur > -- 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] Normal Mode Analysis -- Expected Output
Hello,
I am running a normal mode analysis on a ~1500AA protein with the following
mdp parameters:
Log file opened on Tue Apr 9 09:55:00 2013
Host: uv1 pid: 128985 nodeid: 0 nnodes: 64
Gromacs version:VERSION 4.6.1
Precision: double
Memory model: 64 bit
MPI library:MPI
OpenMP support: disabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library:fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage: enabled
Built on: Fri Mar 15 09:20:59 CDT 2013
Built by: asndcy@uv [CMAKE]
Build OS/arch: Linux 3.0.58-0.6.6-default x86_64
Build CPU vendor: GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz
Build CPU family: 6 Model: 45 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /opt/sgi/mpt/mpt-2.07/bin/mpicc GNU gcc (GCC) 4.7.2
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) VERSION 4.6.1 (-:
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.
:-) /opt/asn/apps/gromacs_4.6.1/bin/mdrun_mpi_d (double precision) (-:
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 ---
Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels
Input Parameters:
integrator = nm
nsteps = 10
init-step= 0
cutoff-scheme= Verlet
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm-mode= Linear
nstlog = 1000
nstxout = 500
nstvout = 500
nstfout = 500
nstcalcenergy= 100
nstenergy= 500
nstxtcout= 0
init-t = 0
delta-t = 0.002
xtcprec = 1000
fourierspacing = 0.12
nkx = 160
nky = 160
nkz = 216
pme-order= 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau-p= 1
ref-p (3x3):
ref-p[0]={ 1.0
[gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)
Hello, I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The ATP residue is stored in a toppar stream file in CHARMM, thus it is not included in the download on the user-submission page for FFs. It also appears that it is not available in the AMBER forcefields. It is however, present in the GROMOS FF supplied with GROMACS and also available on the user-submission website. However, I have reservations about using a united-atom FF in conjunction with CHARMM (which is how the rest of my system is parameterized). I've also taken a PDB of ATP and parameterized it with SWISS-PARAM, however the user-submitted 'CHARMM2GROMACS' scripts are not successfully parsing the topology/parameter files and not generating valid GROMACS output. If anyone has a CHARMM FF for ATP that is in >GROMACS4.5.4 format, I would be much obliged. If it is not available, I could use some help in understanding how to convert toppar stream entries from CHARMM into the GROMACS format. Thank you, Bryan Roessler The University of Alabama-Birmingham -- 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
