Re: [gmx-users] segmentation fault from power6 kernel
Hi Mark, today I tested the 4.5.5 version. It seems here there's not that problem. Anyway, I will take some days to make more tests. Thank you, Fabio - Messaggio originale - Da: "Mark Abraham" A: "Discussion list for GROMACS users" Inviato: Giovedì, 3 novembre 2011 14:40:39 Oggetto: Re: [gmx-users] segmentation fault from power6 kernel On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org including your observations and a .tpr that will reproduce them. Thanks, Mark Fabio The most likely issue is some normal "blowing up" scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault from power6 kernel
Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Fabio The most likely issue is some normal "blowing up" scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] segmentation fault from power6 kernel
Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with
TotalView and I've found that this segmentation violation originates in the
pwr6kernel310.F
Up to now, I still didn't find what is behind this seg violation. I would like
to ask if anybody is aware of a bug behind this function.
The simulation is obtained by using Gromacs 4.5.3 compiled in double precision.
The options that I specified in the configure are:
--disable-threads --enable-power6 --enable-mpi
The log file doesn't provide much informations:
Log file opened on Wed Nov 2 20:11:02 2011
Host: sp0202 pid: 11796682 nodeid: 0 nnodes: 1
The Gromacs distribution was built Thu Dec 16 14:44:40 GMT+01:00 2010 by
propro01@sp0201 (AIX 1 00C3E6444C00)
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.3 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, 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) 2001-2010, 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 General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_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 ---
Input Parameters:
integrator = md
nsteps = 250
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 2500
nstxout = 2500
nstvout = 2500
nstfout = 0
nstcalcenergy= 10
nstenergy= 2500
nstxtcout= 2500
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 50
nky = 50
nkz = 50
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 = Nose-Hoover
nsttcouple = 10
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist
Re: [gmx-users] genconf and bonded interactions
Ok, the problem is solved. Thank you. Fabio On 07/27/2011 05:17 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: Thanks. This actually solved the problem in grompp. I still have problems when running. This is the log of mdrun: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.583 nm, LJ-14, atoms 28051 28056 multi-body bonded interactions: 0.583 nm, Proper Dih., atoms 28051 28056 Minimum cell size due to bonded interactions: 0.642 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm Estimated maximum distance required for P-LINCS: 1.139 nm This distance will limit the DD cell size, you can override this with -rcon Guess for relative PME load: 0.43 Will use 2400 particle-particle and 1696 PME only nodes This is a guess, check the performance at the end of the log file Using 1696 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2400 cells with a minimum initial size of 1.424 nm The maximum allowed number of cells is: X 18 Y 18 Z 6 --- Program mdrun_mpi_bg, VERSION 4.5.4 Source code file: domdec.c, line: 6438 Fatal error: There is no domain decomposition for 2400 nodes that is compatible with the given box and a minimum cell size of 1.4242 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Meet Me At the Coffee Shop" (Red Hot Chili Peppers) I imagine that now I have to tune the dds and rcon parameter. Am I right? I've never touched those parameters and I do not know how they will affect performance or the stability of your systems. The easier solution is to simply reduce the number of processors so that the cell sizes increase a bit. http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm -Justin -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
Thanks. This actually solved the problem in grompp. I still have problems when running. This is the log of mdrun: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.583 nm, LJ-14, atoms 28051 28056 multi-body bonded interactions: 0.583 nm, Proper Dih., atoms 28051 28056 Minimum cell size due to bonded interactions: 0.642 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm Estimated maximum distance required for P-LINCS: 1.139 nm This distance will limit the DD cell size, you can override this with -rcon Guess for relative PME load: 0.43 Will use 2400 particle-particle and 1696 PME only nodes This is a guess, check the performance at the end of the log file Using 1696 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2400 cells with a minimum initial size of 1.424 nm The maximum allowed number of cells is: X 18 Y 18 Z 6 --- Program mdrun_mpi_bg, VERSION 4.5.4 Source code file: domdec.c, line: 6438 Fatal error: There is no domain decomposition for 2400 nodes that is compatible with the given box and a minimum cell size of 1.4242 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Meet Me At the Coffee Shop" (Red Hot Chili Peppers) I imagine that now I have to tune the dds and rcon parameter. Am I right? Fabio On 07/27/2011 04:48 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: This is the key part: processing coordinates... Warning: atom name 18113 in topol.top and out.gro does not match (MN1 - CN1) Warning: atom name 18114 in topol.top and out.gro does not match (MN2 - CN2) Warning: atom name 18115 in topol.top and out.gro does not match (N - CN3) Warning: atom name 18116 in topol.top and out.gro does not match (H1 - N) Warning: atom name 18117 in topol.top and out.gro does not match (H2 - CA) Warning: atom name 18118 in topol.top and out.gro does not match (H3 - CB) Warning: atom name 18119 in topol.top and out.gro does not match (CA - OA) Warning: atom name 18120 in topol.top and out.gro does not match (HA - P) Warning: atom name 18121 in topol.top and out.gro does not match (MCB1 - OB) Warning: atom name 18122 in topol.top and out.gro does not match (MCB2 - OC) Warning: atom name 18123 in topol.top and out.gro does not match (CB - OD) Warning: atom name 18124 in topol.top and out.gro does not match (HB1 - CC) Warning: atom name 18125 in topol.top and out.gro does not match (HB2 - CD) Warning: atom name 18126 in topol.top and out.gro does not match (HB3 - OE) Warning: atom name 18127 in topol.top and out.gro does not match (C - C1A) Warning: atom name 18128 in topol.top and out.gro does not match (O - O1A) Warning: atom name 18129 in topol.top and out.gro does not match (N - C1B) Warning: atom name 18130 in topol.top and out.gro does not match (H - C1C) Warning: atom name 18131 in topol.top and out.gro does not match (CA - C1D) Warning: atom name 18132 in topol.top and out.gro does not match (HA - C1E) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 50]: 219116 non-matching atom names atom names from topol.top will be used atom names from out.gro will be ignored This is the root of the problem. Your topology does not match your coordinates in terms of the order of the molecules. grompp (and, in then later, mdrun) thinks that protein is lipid, lipids are water, etc, so you're effectively telling it that things are bonded within a molecule when they're not. Even if the simulation initially ran it would blow up immediately because you're mapping the wrong coordinates onto the wrong molecules. The coordinate file from genconf is an exact replica of your system, but the molecules are not re-ordered in any convenient way. So, for your system, instead of: [ molecules ] Protein_A 4N Protein_B 4N Protein_C 4N Protein_D 4N POPC 4N POPG 4N SOL 4N K+ 4N you need this in your topology: [ molecules ] Protein_A N Protein_B N Protein_C N Protein_D N POPC N POPG N SOL N K+ N (repeated three more times) Otherwise, reorganize the .gro file. Topology manipulation is probably easier, though. -Justin -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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_Li
Re: [gmx-users] genconf and bonded interactions
On 07/27/2011 04:12 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/27/2011 03:54 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 30.031 nm, LJ-14, atoms 40702 40705 multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704 Minimum cell size due to bonded interactions: 33.035 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm Estimated maximum distance required for P-LINCS: 1.139 nm Guess for relative PME load: 0.43 Will use 2400 particle-particle and 1696 PME only nodes This is a guess, check the performance at the end of the log file Using 1696 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2400 cells with a minimum initial size of 41.293 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun_mpi_bg, VERSION 4.5.4 Source code file: domdec.c, line: 6438 Fatal error: There is no domain decomposition for 2400 nodes that is compatible with the given box and a minimum cell size of 41.2932 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is bizarre. Did you fix the periodicity of the original coordinate file (conf_start.gro) and rebuild the system, or did you try to run trjconv on the replicated system? The former is the correct approach. -Justin This is what I did (in the chronological order): 1) trjconv -f conf_start.gro -o conf_whole.gro -pbc whole Presumably in conjunction with a .tpr file, in order for this to work? Ok, I added. 2) genconf -f conf_whole.gro -o out.gro -nbox 2 2 1 3) i modified the topol.top (modifying the number of molecules) 4) grompp -f grompp.mdp -c out.gro -p topol.top -maxwarn 3 What are the warnings you are trying to circumvent? Please provide the full grompp output. I can think of a few other possibilities for the source of your problem, but I do not want to venture idle guesswork without seeing all of the warnings you've got. This is the full grompp output: :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, 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 General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: Option Filename Type Description -f grompp.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -cout.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p topol.top InputTopology file -pp processed.top Output, Opt. Topology file -o topol.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int3 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'dihre-tau' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Re: [gmx-users] genconf and bonded interactions
On 07/27/2011 03:54 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 30.031 nm, LJ-14, atoms 40702 40705 multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704 Minimum cell size due to bonded interactions: 33.035 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm Estimated maximum distance required for P-LINCS: 1.139 nm Guess for relative PME load: 0.43 Will use 2400 particle-particle and 1696 PME only nodes This is a guess, check the performance at the end of the log file Using 1696 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2400 cells with a minimum initial size of 41.293 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun_mpi_bg, VERSION 4.5.4 Source code file: domdec.c, line: 6438 Fatal error: There is no domain decomposition for 2400 nodes that is compatible with the given box and a minimum cell size of 41.2932 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is bizarre. Did you fix the periodicity of the original coordinate file (conf_start.gro) and rebuild the system, or did you try to run trjconv on the replicated system? The former is the correct approach. -Justin This is what I did (in the chronological order): 1) trjconv -f conf_start.gro -o conf_whole.gro -pbc whole 2) genconf -f conf_whole.gro -o out.gro -nbox 2 2 1 3) i modified the topol.top (modifying the number of molecules) 4) grompp -f grompp.mdp -c out.gro -p topol.top -maxwarn 3 5) launched mdrun Fabio -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
On 07/27/2011 03:38 PM, Justin A. Lemkul wrote: Please make sure to keep the discussion on the list. Sorry, I just was continuing the discussion after sending you my coordinates. Fabio Affinito wrote: Justin, first of all, I thank you very much for your help: it's very precious. I regret I didn't notice before the molecule was broken. I suggested to you yesterday that your initial configuration was broken. You told me it wasn't. I checked with VMD but I was in error. I acknowledged my error, I think. Didn't I? Unfortunately the problem is not solved with your recipe. I used trjconv on the starting configuration and then I used the genconf. The mdrun fails with the same error. In this case, the atoms involved in the error are not the same of the previous one. But once again the bond length is completely odd. During the grompp I had some warning, but I can't understand where they are coming from: Certain bonded interactions can't take place between massless particles. As the warning states, if pdb2gmx produced the topology, don't worry about it. Cleaning up constraints and constant bonded interactions with virtual sites Removed 1305 Angles with virtual sites, 6251 left Removed 480 Proper Dih.s with virtual sites, 363 left Converted 2230 Constraints with virtual sites to connections, 2596 left Warning: removed 582 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1305 Angles with virtual sites, 6251 left Removed 480 Proper Dih.s with virtual sites, 363 left Converted 2230 Constraints with virtual sites to connections, 2596 left Warning: removed 582 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1305 Angles with virtual sites, 6251 left Removed 480 Proper Dih.s with virtual sites, 363 left Converted 2230 Constraints with virtual sites to connections, 2596 left Warning: removed 582 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning Cleaning up constraints and constant bonded interactions with virtual sites Removed 1305 Angles with virtual sites, 6251 left Removed 480 Proper Dih.s with virtual sites, 363 left Converted 2230 Constraints with virtual sites to connections, 2596 left Warning: removed 582 Constraints with vsite with Virtual site 3out construction This vsite construction does not guarantee constant bond-length If the constructions were generated by pdb2gmx ignore this warning According to your experience, this can be pertinent with my problems? Not likely. The virtual sites are within the protein, not the lipids, right? Without the mdrun output, there's little else I can tell you. This is the mdrun output: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 30.031 nm, LJ-14, atoms 40702 40705 multi-body bonded interactions: 30.031 nm, Angle, atoms 40701 40704 Minimum cell size due to bonded interactions: 33.035 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm Estimated maximum distance required for P-LINCS: 1.139 nm Guess for relative PME load: 0.43 Will use 2400 particle-particle and 1696 PME only nodes This is a guess, check the performance at the end of the log file Using 1696 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2400 cells with a minimum initial size of 41.293 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun_mpi_bg, VERSION 4.5.4 Source code file: domdec.c, line: 6438 Fatal error: There is no domain decomposition for 2400 nodes that is compatible with the given box and a minimum cell size of 41.2932 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Fabio -Justin Thank you once again, Fabio On 07/27/2011 02:45 PM, Justin A. Lemkul wrote: The problem is indeed as I suspected. Your molecules are broken across periodic boundaries in the initial configuration. When you replicate with genbox, you've now replicated broken molecules
Re: [gmx-users] genconf and bonded interactions
On 07/26/2011 07:02 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 05:06 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: Maybe this is a different issue... but it's ok that after the 99,999th atom the counter restarts from zero? 21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977 21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638 Could this be the origin of my problem? Atom numbering is not the problem. This happens all the time for systems of hundreds of thousands of atoms, which Gromacs handles just fine. Please investigate the points I suggested before. Yes, but this doesn't make things easier! :-) According to the log the atoms to consider are 159986 and 159990 That's not what you posted before. The .log output indicated atoms 193657 and 193660 were problematic. Sorry. It's because I've tried with many systems (with different -nbox values) and the error was always the same. Browsing the conf.gro, if I didn't make mistakes this atoms are: 30040POPG OE59986 0.080 13.158 2.964 0.0885 0.4154 -0.0859 30040POPG C1C59990 0.219 26.034 3.221 0.6449 0.0750 0.1313 But their distance is 12.8nm, while md.log reports 38.911 nm... In any case, why are atoms four bonds (based on the original .log output of 1-4 interactions being a problem) away separated by 12.8 nm? Seems very odd to me. I ask yet again - what are your box vectors, before and after manipulation with genconf? Seems odd to me, too. For the box vectors (sorry if I didnt answer before), in this case: after: 26.04658 26.04658 8.75317 before: 13.02329 13.02329 8.75317 Hope it helps. Best regards, Fabio -Justin So what? F. -Justin Thanks again, Fabio On 07/26/2011 04:38 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:30 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:19 PM, Justin A. Lemkul wrote: Were the molecules whole in the coordinate file you replicated? If not, the bonds will now be assigned across the entire box. -Justin Yes and not, depending on what you mean by "whole". It is an ion channel, so it's made of four chains. This clarifies? (i guess not..) By whole, I mean that the molecules are not split across periodic boundaries in the initial configuration that you replicated. If you replicate a periodic break, then you split the molecules by a distance equal to the new periodic distance. -Justin Ok, so: no, it's not broken. What you need to do is use the information mdrun provided you to diagnose what's going on. Apparently atoms 193657 193660 are separated by 31 nm. What are your box vectors? Where are these atoms in the system? Then you'll have your answer. The only reason I can think of for such extreme distances is a periodicity issue. -Justin -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: Maybe this is a different issue... but it's ok that after the 99,999th atom the counter restarts from zero? 21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977 21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638 Could this be the origin of my problem? Atom numbering is not the problem. This happens all the time for systems of hundreds of thousands of atoms, which Gromacs handles just fine. Please investigate the points I suggested before. Yes, but this doesn't make things easier! :-) According to the log the atoms to consider are 159986 and 159990 Browsing the conf.gro, if I didn't make mistakes this atoms are: 30040POPGOE59986 0.080 13.158 2.964 0.0885 0.4154 -0.0859 30040POPG C1C59990 0.219 26.034 3.221 0.6449 0.0750 0.1313 But their distance is 12.8nm, while md.log reports 38.911 nm... So what? F. -Justin Thanks again, Fabio On 07/26/2011 04:38 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:30 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:19 PM, Justin A. Lemkul wrote: Were the molecules whole in the coordinate file you replicated? If not, the bonds will now be assigned across the entire box. -Justin Yes and not, depending on what you mean by "whole". It is an ion channel, so it's made of four chains. This clarifies? (i guess not..) By whole, I mean that the molecules are not split across periodic boundaries in the initial configuration that you replicated. If you replicate a periodic break, then you split the molecules by a distance equal to the new periodic distance. -Justin Ok, so: no, it's not broken. What you need to do is use the information mdrun provided you to diagnose what's going on. Apparently atoms 193657 193660 are separated by 31 nm. What are your box vectors? Where are these atoms in the system? Then you'll have your answer. The only reason I can think of for such extreme distances is a periodicity issue. -Justin -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
Maybe this is a different issue... but it's ok that after the 99,999th atom the counter restarts from zero? 21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977 21374SOLHW10 13.069 8.987 7.081 0.5916 0.5409 0.0638 Could this be the origin of my problem? Thanks again, Fabio On 07/26/2011 04:38 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:30 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:19 PM, Justin A. Lemkul wrote: Were the molecules whole in the coordinate file you replicated? If not, the bonds will now be assigned across the entire box. -Justin Yes and not, depending on what you mean by "whole". It is an ion channel, so it's made of four chains. This clarifies? (i guess not..) By whole, I mean that the molecules are not split across periodic boundaries in the initial configuration that you replicated. If you replicate a periodic break, then you split the molecules by a distance equal to the new periodic distance. -Justin Ok, so: no, it's not broken. What you need to do is use the information mdrun provided you to diagnose what's going on. Apparently atoms 193657 193660 are separated by 31 nm. What are your box vectors? Where are these atoms in the system? Then you'll have your answer. The only reason I can think of for such extreme distances is a periodicity issue. -Justin -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote: Fabio Affinito wrote: On 07/26/2011 04:19 PM, Justin A. Lemkul wrote: Were the molecules whole in the coordinate file you replicated? If not, the bonds will now be assigned across the entire box. -Justin Yes and not, depending on what you mean by "whole". It is an ion channel, so it's made of four chains. This clarifies? (i guess not..) By whole, I mean that the molecules are not split across periodic boundaries in the initial configuration that you replicated. If you replicate a periodic break, then you split the molecules by a distance equal to the new periodic distance. -Justin Ok, so: no, it's not broken. -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote: Were the molecules whole in the coordinate file you replicated? If not, the bonds will now be assigned across the entire box. -Justin Yes and not, depending on what you mean by "whole". It is an ion channel, so it's made of four chains. This clarifies? (i guess not..) F -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] genconf and bonded interactions
Hi all, I used genconf because I wanted to replicate a membrane with ion channel on the xy plane: genconf -f conf.gro -o out.gro -nbox 2 2 1 Then I edited by hand the .top file where I modified the number of molecules in the system. When attempting to run, disregarding the number of processors, the mdrun crashes because domain decomposition fails. Looking with attention to the log I find this: Initializing Domain Decomposition on 4096 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660 multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659 Minimum cell size due to bonded interactions: 33.959 nm Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm Estimated maximum distance required for P-LINCS: 1.139 nm Guess for relative PME load: 0.44 Will use 2304 particle-particle and 1792 PME only nodes This is a guess, check the performance at the end of the log file Using 1792 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2304 cells with a minimum initial size of 42.448 nm The maximum allowed number of cells is: X 1 Y 1 Z 0 Now, I'm wondering why do I have such big bond interation length.. 31nm! I guess that the problems in the DD arises from this. Can you give me some suggestions? Thanks in advance, Fabio -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] scaling of replica exchange
Hi Mark, I've checked with Valeria and the problem is actually on the setup of the system (unfair overlapping of the temperature distribution). So I think that the loss of efficiency should be of a factor between 2 or 3 in her case and not more. Bye, Fabio On 02/23/2011 10:31 AM, Mark Abraham wrote: > > > On 02/23/11, *Valeria Losasso * wrote: >> >> Thank you Mark. I found one message of this month concerning this >> topic, and there are some small suggestions. I don't think that such a >> changes can restore a factor of 26, but it could be worth to try to >> see what happens. I will let you know. > > They won't. The problem is that every 10 (or so) MD steps every > processor does global communication to check nothing's gone wrong. That > resulted from some unrelated bits of code trying to share the same > machinery for efficiency, and treading on each others' toes. > > Mark > >> Valeria >> >> >> >> On Wed, 23 Feb 2011, Mark Abraham wrote: >> >> > >> > >> >On 02/23/11, Valeria Losasso wrote: >> > >> > Dear all, >> > I am making some tests to start using replica exchange >> molecular dynamics on my system in water. The setup is ok >> > (i.e. one replica alone runs correctly), but I am not able to >> parallelize the REMD. Details follow: >> > >> > - the test is on 8 temperatures, so 8 replicas >> > - Gromacs version 4.5.3 >> > - One replica alone, in 30 minutes with 256 processors, makes >> 52500 steps. 8 replicas with 256x8 = 2048 >> > processors, make 300 (!!) steps each = 2400 in total (I arrived >> to these numbers just to see some update of the >> > log file: since I am running on a big cluster, I can not use >> more than half an hour for tests with less than 512 >> > processors) >> > - I am using mpirun with options -np 256 -s md_.tpr -multi 8 >> -replex 1000 >> > >> > >> >There have been two threads on this topic in the last month or so, >> please check the archives. The implementation of >> >multi-simulations scales poorly. The scaling of replica-exchange >> itself is not great either. I have a working version under >> >final development that scales much better. Watch this space. >> > >> >Mark >> > -- * Fabio Affinito, PhD CINECA SuperComputing Applications and Innovation Department - SCAI Via Magnanelli, 6/3 40033 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) -- 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] domain decomposition error
Hi, I'm trying to run a simulation with 4.5.3 (double precision) on bluegene. I get this error: > NOTE: Turning on dynamic load balancing > > vol 0.35! imb F 54% pme/F 2.06 step 100, remaining runtime: 3 s > vol 0.33! imb F 48% pme/F 2.09 step 200, remaining runtime: 2 s > vol 0.35! imb F 28% pme/F 2.42 step 300, remaining runtime: 1 s > vol 0.34! imb F 26% pme/F 2.46 step 400, remaining runtime: 0 s > > --- > Program mdrun_mpi_bg_d, VERSION 4.5.3 > Source code file: domdec.c, line: 3581 > > Fatal error: > Step 490: The X-size (0.78) times the triclinic skew factor (1.00) is > smaller than the smallest allowed cell size (0.80) for domain > decomposition grid cell 4 2 2 > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > "Everything's formed from particles" (Van der Graaf Generator) > > Error on node 188, will try to stop all the nodes > Halting parallel program mdrun_mpi_bg_d on CPU 188 out of 256 > Can anybody give me some hint about that? Thanks in advance, Fabio -- * Fabio Affinito, PhD CINECA SuperComputing Applications and Innovation Department - SCAI Via Magnanelli, 6/3 40033 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) -- 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] problem linking fftw2 with gromacs 4.5.3
Hi folks, I'm experiencing some problem when I try to compile gromacs 4.5.3 linking fftw. This is the configure: > ./configure --prefix=/bgp/userinternal/cin0644a/gromacs.453 \ > --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \ > --disable-ppc-altivec \ > --enable-bluegene --enable-mpi --with-fft=fftw2 \ > --program-suffix=_mpi_bg_dp \ > --without-x \ > CC=mpixlc_r \ > CFLAGS="-O3 -qarch=450d -qtune=450" \ > MPICC=mpixlc_r CXX=mpixlC_r \ > CXXFLAGS="-O3 -qarch=450d -qtune=450" \ > CPPFLAGS="-I/bgp/userinternal/cin0644a/fftw2/include" \ > F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \ > LDFLAGS="-L/bgp/userinternal/cin0644a/fftw2/lib" This is the error during the make > mkdir .libs > libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled > argument `../mdlib/libmd_mpi.la' > make[1]: *** [libgmxpreprocess_mpi.la] Error 1 > make[1]: Leaving directory > `/bgp/userinternal/cin0644a/gromacs-4.5.3/src/kernel' The directory /lib: > libfftw.a libfftw_threads.a librfftw.a librfftw_threads.a > libfftw.la libfftw_threads.la librfftw.la librfftw_threads.la The directory /include: > fftw.h fftw_threads.h rfftw.h rfftw_threads.h Do you have any hint? Thanks in advance, Fabio -- * Fabio Affinito, PhD CINECA SuperComputing Applications and Innovation Department - SCAI Via Magnanelli, 6/3 40033 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) -- 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] problem linking fftw2 with gromacs 4.5.3
Sorry, Mark, the problem was in fact in the compilation of fftw. I solved everything by compiling them in the most simple way: ./configure --prefix=whatelse and now everything works fine. Thank you On 11/16/2010 04:18 PM, Mark Abraham wrote: > > > - Original Message - > From: Fabio Affinito > Date: Wednesday, November 17, 2010 1:58 > Subject: [gmx-users] problem linking fftw2 with gromacs 4.5.3 > To: gmx-users@gromacs.org > >> Hi folks, >> I'm experiencing some problem when I try to compile gromacs 4.5.3 >> linking fftw. >> This is the configure: >> > ./configure --prefix=/bgp/userinternal/cin0644a/gromacs.453 \ >> > --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \ >> > --disable-ppc-altivec \ >> > --enable-bluegene --enable-mpi --with-fft=fftw2 \ >> > --program-suffix=_mpi_bg_dp \ >> > --without-x \ >> > CC=mpixlc_r \ >> > CFLAGS="-O3 -qarch=450d -qtune=450" \ >> > MPICC=mpixlc_r CXX=mpixlC_r \ >> > CXXFLAGS="-O3 -qarch=450d -qtune=450" \ >> > CPPFLAGS="-I/bgp/userinternal/cin0644a/fftw2/include" \ >> > F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \ >> > LDFLAGS="-L/bgp/userinternal/cin0644a/fftw2/lib" >> >> This is the error during the make >> > mkdir .libs >> > libtool: link: cannot find the library `../mdlib/libmd_mpi.la' >> or unhandled argument `../mdlib/libmd_mpi.la' >> > make[1]: *** [libgmxpreprocess_mpi.la] Error 1 >> > make[1]: Leaving directory `/bgp/userinternal/cin0644a/gromacs- >> 4.5.3/src/kernel' >> The directory /lib: >> >> > libfftw.a libfftw_threads.a >> librfftw.a librfftw_threads.a >> > libfftw.la libfftw_threads.la librfftw.la >> librfftw_threads.la >> The directory /include: >> >> > fftw.h fftw_threads.h rfftw.h rfftw_threads.h >> >> Do you have any hint? > > I'd be looking for errors higher up in the output, where > mdlib/libmd_mpi.la got (not) made. > > Mark > >> >> Thanks in advance, >> >> Fabio >> >> >> >> -- >> * >> Fabio Affinito, PhD >> CINECA >> SuperComputing Applications and Innovation Department - SCAI >> Via Magnanelli, 6/3 >> 40033 Casalecchio di Reno (Bologna) ITALY >> +39/051/6171794 (Phone) >> -- >> 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 > -- * Fabio Affinito, PhD CINECA SuperComputing Applications and Innovation Department - SCAI Via Magnanelli, 6/3 40033 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) -- 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] g_cluster: optimal cutoff
On 10/31/2010 08:20 PM, Valeria Losasso wrote: > Dear all, > for my cluster analysis I am using the g_cluster tool with the gromos method. > The problem is that I have to compare the results for system of different > lengths, and of course the result of the cluster analysis changes according > to the cutoff chosen. So what will be a great choice in this case? > I was thinking about different possibilities, namely: i) choosing - as it is > quite frequent in the literature - an arbitrary cutoff (like the default > 0.1), but using the same for different systems would be probably not > suitable... > ii) looking for every case at the RMSD distribution and choosing the minimum > value between the two peaks - in this case the cutoff would vary for every > system; iii) choosing for every system the cutoff that allows to have in the > largest cluster the 50% of the structures, and also in this case the cutoff > would be different for the different cases... > > Any hint? > Thanks a lot, > Valeria > > > Option ii) is the right one. Fabio -- * Fabio Affinito, PhD CINECA SuperComputing Applications and Innovation Department - SCAI Via Magnanelli, 6/3 40033 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) -- 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] ffyw3f library not found..
Hi Mark, thanks for the explanation. Anyway, I had this kind of problem only when configuring for the frontend, whilst everything was ok with fftw3 when I configured and compiled for the computation nodes. Fabio On 09/23/2010 03:20 PM, Mark Abraham wrote: > > > - Original Message - > From: Fabio Affinito > Date: Thursday, September 23, 2010 20:54 > Subject: Re: [gmx-users] ffyw3f library not found.. > To: Discussion list for GROMACS users > >> On 09/23/2010 12:27 PM, Kamalesh Roy wrote: >> > Dear users >> > >> > I am trying to install Gromacs-4.5 with fftw-3.2.2 in >> Fedora version 9, >> > when I am trying to install the Groamcs >> > after installing fftw it is giving me an error that ftwf >> library not found. >> > >> > Please hep me. >> > >> > -- >> > Regards >> > Kamalesh Roy >> > >> >> Same problem here. >> Using: >> ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \ >> --enable-ppc-sqrt \ >> --disable-ppc-altivec \ >> --with-fft=fftw3 \ >> --without-x \ >> CFLAGS="-O3 -qarch=auto -qtune=auto" \ >> CC="xlc_r -q64" \ >> CXX="xlC_r -q64" \ >> CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ >> CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ >> F77="xlf_r -q64" \ >> FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ >> LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" >> is fine with 4.0.7 but it generates >> checking for main in -lfftw3f... no >> configure: error: Cannot find fftw3f library >> in 4.5.1 >> >> I successfully installed 4.5.1 only using the --with-fft=fftpack > > Don't use that, it will be diabolically slow for PME simulations! > > Unfortunately, the BlueGene-specific GROMACS installation instructions > didn't have the clue that the precision of GROMACS and FFTW has to > match. It does now. > > Presumably both you and the original poster need to install a > single-precision copy of FFTW, or configure a double-precision version > of GROMACS (if you know you need double precision, or don't mind your > simulation being much slower). > > Mark > -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] fftw and configure in 4.0.7 vs 4.5.1
Hi everybody, I'm experiencing several problems by running configure in 4.5.1. More specifically, it seems it doesn't find fftw libraries. It seems strange 'cause the same options used in 4.0.7 work fine. These are my configure flags: ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --with-fft=fftw3 \ --without-x \ --enable-shared \ CFLAGS="-O3 -qarch=auto -qtune=auto" \ CC="xlc_r -q64" \ CXX="xlC_r -q64" \ CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ F77="xlf_r -q64" \ FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" This is my error in 4.5.1 checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library Whilst in 4.0.7 everything works. Any hints? Thanks in advance, Fabio -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] ffyw3f library not found..
On 09/23/2010 12:27 PM, Kamalesh Roy wrote: > Dear users > > I am trying to install Gromacs-4.5 with fftw-3.2.2 in Fedora version 9, > when I am trying to install the Groamcs > after installing fftw it is giving me an error that ftwf library not found. > > Please hep me. > > -- > Regards > Kamalesh Roy > Same problem here. Using: ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --with-fft=fftw3 \ --without-x \ CFLAGS="-O3 -qarch=auto -qtune=auto" \ CC="xlc_r -q64" \ CXX="xlC_r -q64" \ CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ F77="xlf_r -q64" \ FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" is fine with 4.0.7 but it generates checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library in 4.5.1 I successfully installed 4.5.1 only using the --with-fft=fftpack Fabio -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] error on compilation on BlueGene/P
Like for the frontend, the --enable-fortran is the problem. Maybe it could be useful to update the instruction page :) Fabio On 09/21/2010 10:54 AM, Mark Abraham wrote: > > > - Original Message - > From: Fabio Affinito > Date: Tuesday, September 21, 2010 18:51 > Subject: Re: [gmx-users] error on compilation on BlueGene/P > To: Discussion list for GROMACS users > >> Thank you, Mark and Berk! >> your suggestion was helpful and I successfully compiled on the >> frontend.Now I have a problem when I compile on the compute nodes. >> Configure was fine with these parameters: >> >> ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ >> --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \ >> --disable-ppc-altivec \ >> --enable-bluegene --enable-fortran --enable-mpi \ >> --with-fft=fftw3 \ >> --program-suffix=_mpi_bg \ >> --without-x \ >> CC=mpixlc_r \ >> CFLAGS="-O3 -qarch=450d -qtune=450" \ >> MPICC=mpixlc_r CXX=mpixlC_r \ >> CXXFLAGS="-O3 -qarch=450d -qtune=450" \ >> CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ >> F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \ >> LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" \ >> LIBS="-lmass" >> >> But when I compile using "make mdrun" the compilation stops in >> this way. >> >> creating libgmxpreprocess_mpi.la >> (cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s >> ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la) >> make[1]: *** No rule to make target `../mdlib/libmd_mpi.la', >> needed by >> `mdrun'. Stop. >> make[1]: Leaving directory >> `/bgp/userinternal/cin0644a/gmx/bgp/src/kernel' >> Any suggestion? Thanks! > > > Normally that would be symptomatic of an earlier error in make (or maybe > configure). Please check carefully. > > Mark > -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] error on compilation on BlueGene/P
Thank you, Mark and Berk! your suggestion was helpful and I successfully compiled on the frontend. Now I have a problem when I compile on the compute nodes. Configure was fine with these parameters: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \ --disable-ppc-altivec \ --enable-bluegene --enable-fortran --enable-mpi \ --with-fft=fftw3 \ --program-suffix=_mpi_bg \ --without-x \ CC=mpixlc_r \ CFLAGS="-O3 -qarch=450d -qtune=450" \ MPICC=mpixlc_r CXX=mpixlC_r \ CXXFLAGS="-O3 -qarch=450d -qtune=450" \ CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \ LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" \ LIBS="-lmass" But when I compile using "make mdrun" the compilation stops in this way. creating libgmxpreprocess_mpi.la (cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s ../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la) make[1]: *** No rule to make target `../mdlib/libmd_mpi.la', needed by `mdrun'. Stop. make[1]: Leaving directory `/bgp/userinternal/cin0644a/gmx/bgp/src/kernel' Any suggestion? Thanks! Fabio On 09/21/2010 12:03 AM, Mark Abraham wrote: > Hi, > > IIRC GROMACS has done something radical to FORTRAN inner loops (like > removing them) since those instructions were written. Removing > --enable-fortran will make your symptoms go away. The C inner loops will > be fine, should you ever be running mdrun on the front end nodes. > >> ... and if I add the --enable-bluegene flag : >> >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h", >> line 163.21: 1506-1231 (S) The built-in function "__fpsub" is >> not valid >> for the target architecture. >> >> and more similar errors. > > Sure. --enable-bluegene is only useful for the mdrun binary for the > compute system. > > Mark > >> On 09/20/2010 05:35 PM, Fabio Affinito wrote: >> > Hi all, >> > I'm trying to install Gromacs on BG/P following the >> instruction reported >> > here: >> > >> > http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene> > >> > I ran configure: >> > ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ >> > --enable-ppc-sqrt \ >> > --disable-ppc-altivec \ >> > --enable-fortran \ >> > --with-fft=fftw3 \ >> > --without-x \ >> > CFLAGS="-O3 -qarch=auto -qtune=auto" \ >> > CC="xlc_r -q64" \ >> > CXX="xlC_r -q64" \ >> > CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ >> > CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ >> > F77="xlf_r -q64" \ >> > FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ >> > LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" >> > >> > But when I compile with make I get this error: >> > >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",> > line 42.10: 1506-296 (S) #include file "nbkernel010_f77_single.h" not found. >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",> > line 43.10: 1506-296 (S) #include file "nbkernel020_f77_single.h" not found. >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",> > line 44.10: 1506-296 (S) #include file "nbkernel030_f77_single.h" not found. >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",> > line 45.10: 1506-296 (S) #include file "nbkernel100_f77_single.h" not found. >> > [...] >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",> > line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",> > line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. >> > >> > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_
Re: [gmx-users] error on compilation on BlueGene/P
... and if I add the --enable-bluegene flag : "../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h", line 163.21: 1506-1231 (S) The built-in function "__fpsub" is not valid for the target architecture. and more similar errors. F. On 09/20/2010 05:35 PM, Fabio Affinito wrote: > Hi all, > I'm trying to install Gromacs on BG/P following the instruction reported > here: > http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene > > I ran configure: > ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ > --enable-ppc-sqrt \ > --disable-ppc-altivec \ > --enable-fortran \ > --with-fft=fftw3 \ > --without-x \ > CFLAGS="-O3 -qarch=auto -qtune=auto" \ > CC="xlc_r -q64" \ > CXX="xlC_r -q64" \ > CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ > CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ > F77="xlf_r -q64" \ > FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ > LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" > > But when I compile with make I get this error: > > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 42.10: 1506-296 (S) #include file "nbkernel010_f77_single.h" not found. > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 43.10: 1506-296 (S) #include file "nbkernel020_f77_single.h" not found. > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 44.10: 1506-296 (S) #include file "nbkernel030_f77_single.h" not found. > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 45.10: 1506-296 (S) #include file "nbkernel100_f77_single.h" not found. > [...] > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single. > "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", > line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single. > > > Do you have any hint about that? > > Thanks in advance! > > F. > > -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] error on compilation on BlueGene/P
Hi all, I'm trying to install Gromacs on BG/P following the instruction reported here: http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene I ran configure: ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CFLAGS="-O3 -qarch=auto -qtune=auto" \ CC="xlc_r -q64" \ CXX="xlC_r -q64" \ CXXFLAGS="-O3 -qarch=auto -qtune=auto" \ CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \ F77="xlf_r -q64" \ FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \ LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" But when I compile with make I get this error: "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 42.10: 1506-296 (S) #include file "nbkernel010_f77_single.h" not found. "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 43.10: 1506-296 (S) #include file "nbkernel020_f77_single.h" not found. "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 44.10: 1506-296 (S) #include file "nbkernel030_f77_single.h" not found. "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 45.10: 1506-296 (S) #include file "nbkernel100_f77_single.h" not found. [...] "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single. "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single. "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single. "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c", line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single. Do you have any hint about that? Thanks in advance! F. -- * Fabio Affinito, PhD CINECA InterUniversity Computer Center Via Magnanelli, 6/3 Casalecchio di Reno (Bologna) ITALY +39/051/6171794 (Phone) e-mail: f.affin...@cineca.it -- 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] centering molecule in the water box
Peyman, the protein moves because the c.o.m. motion wasn't subtracted during the dynamics. On Tuesday 01 July 2008 12:24, Fabio Affinito wrote: I think if it moves, then there is something more basic wrong, do you remove your center of mass motion appropriately? is your box homogeneously equilibrated? but if it does not move and it looks like as if it moved, then it's visual problem and not important! you could e.g. write something to cut the solvent molecules from one side and put them on the other side with some mapping dependant on your box type, if you would like to see your molecule at the center. btw, self diffusion is the diffusion of one molecule through others of its own kind, not through other molecules, solvent or else. if there is no chemical potential ( ~concentration ) difference, no mass transfer would take place. Peyman Fabio Affinito, PhD SISSA/ISAS -Statistical and Biological Physics Via Beirut, 4 34014 Trieste ITALY email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] centering molecule in the water box
I choosed "Protein" for centering and "System" for output. Same stuff with editconf. F. Fabio Affinito, PhD email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] centering molecule in the water box
The protein experience self-diffusion and so it moves through the simulation box. I tried also with editconf but the result is the same. F. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] centering molecule in the water box
Hi all, During my MD the molecule experience a drift. Now I want to put the molecule at the center of the water box. I tried with trjconv using the -pbc mol and -center flag and using a reference frame where the molecule is at the center of the box. It seems that all the box (water+molecule) is translated, and so the position of the molecule relatively to the box is unchanged. I also checked the gmx-users list and I didn't get any useful suggestion. Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: RE: [gmx-users] crash nsgrid.c
Hi Berk, thanks for your answer. I've checked the charge groups and every thing seems to be ok (no single groups...). Actually I'm using 3.2.1 version, but it doesn't seem to be depending on that. What could I check? Fabio On May 8, 2008, at 4:00 PM, [EMAIL PROTECTED] wrote: -- Message: 3 Date: Thu, 8 May 2008 15:21:16 +0200 From: Berk Hess <[EMAIL PROTECTED]> Subject: RE: [gmx-users] crash nsgrid.c To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hi,There can be many reasons for such problems.I assume you use solvent.One option is that you could have made your whole proteina single charge group. grompp in Gromacs 3.3.3 checks for this,but older versions do not.Berk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] crash nsgrid.c
Dear all, During my simulations of a GFP protein (force field made with amber, then converted to gromacs), I usually get this error: Fatal error: ci = 8108 should be in 0 .. 7937 [FILE nsgrid.c, LINE 218] What this that means? If I restart the simulation from the frame just before the crash, the run is ok for a (random) time and then it crashes again. I checked this on different kind of machines and I get always the same behavior. To make things clearier, I include the input.mdp file: title= cpp = /lib/cpp include = define = integrator = md dt = 0.002 nsteps = 50 nstxout = 1 nstvout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 500 energygrps = System pbc = xyz nstlist = 15 epsilon_r= 1. ns_type = grid coulombtype = pme vdwtype = Cut-off rlist= 0.8 rcoulomb = 0.8 rvdw = 0.8 tcoupl = Nose-Hoover tc-grps = System tau_t= 2.0 ref_t= 300.00 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p= 4.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_seed = 173529 constraints = All-bonds constraint_algorithm = lincs shake_tol= 0.0001 Any suggestion is welcome. Thanks F.A. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fatal error in nsgrid
I've been running on 16 processors a protein MD simulation. During the simulation I've got a crash and the standard error reported this: Fatal error: ci = 10280 should be in 0 .. 10050 [FILE nsgrid.c, LINE 218] [0] MPI Abort by user Aborting program ! [0] Aborting program! What could that be? Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dPCA - trajectories
On 29/ago/07, at 04:11, Mark Abraham wrote: Dear all, Using g_angle -f ../trj1_0_100.xtc -s ../g_prot.tpr -n test.ndx -or -type dihedral -e 1 g_covar -f traj.trr -s dummy.gro -nofit It seems like the trajectory is of a different length, because a different timestep seems to be used: Well, you are using a different trajectory file... It is different because it is made of angles, not of coordinates. But the length, the numbers of frames and the timestep should be the same. Shouldn't it? Fabio Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Fabio Affinito, PhD SISSA/ISAS - Statistical and Biological Physics Via Beirut, 4 email: [EMAIL PROTECTED] 34014 Trieste phone: +39 040 3787 303 ITALY fax: +39 040 3787 528 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dPCA - trajectories
Dear all, Using g_angle -f ../trj1_0_100.xtc -s ../g_prot.tpr -n test.ndx -or -type dihedral -e 1 As expected, I obtained the following statement [cut] Group 0 (Backbone) has 664 elements There is one group in the index Reading file ../g_prot.tpr, VERSION 3.2.1 (single precision) Last frame 25000 time 1.000 There are 166 dihedrals. Will fill 111 atom positions with cos/sin [cut] Then, when using the covariance analysis g_covar -f traj.trr -s dummy.gro -nofit It seems like the trajectory is of a different length, because a different timestep seems to be used: [cut] Calculating the average structure ... trn version: GMX_trn_file (double precision) Last frame 25000 time 25000.000 Constructing covariance matrix (333x333) ... Last frame 25000 time 25000.000 Read 25001 frames [cut] I suppose it's just because in the new trajectory the information of the timestep length is lost. Am I right? Thank you, Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: mk_angndx
angle multiplicity force constant so, does it refer to the angle values contained in the topology files? Thank you, Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mk_angndx
Hi everybody, what's the meaning of the labels in the angle.ndx generated by the mk_angndx? For example, I've got groups named [ Phi=0.0_3_3.77 ].. what does that mean? Thanks, Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
