Just to be clear, is this the expanded ensemble version of the calculation?
On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > I found the -multi version of that tutorial a bit temperamental... > Michael Shirts suggested that double precision is more reliable for > expanded ensemble. Hopefully he can chime in in a day or two. > > Mark > > On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale > <chris.ne...@mail.utoronto.ca> wrote: >> Dear Users: >> >> Has anyone successfully run the free energy tutorial at >> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy >> ? >> >> I just tried it and I get a segmentation fault immediately (see output at >> the end of this post). >> >> I get a segfault with both 4.6.3 and 4.6.1. >> >> Note that if I modify the .mdp file to set free-energy = no , then the >> simulation runs just fine. (I have, of course, set init-lambda-state in the >> .mdp file that I downloaded from the aforementioned site and I get a >> segfault with any value of init-lambda-state from 0 to 8). >> >> gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg >> :-) G R O M A C S (-: >> >> GROup of MAchos and Cynical Suckers >> >> :-) VERSION 4.6.3 (-: >> >> 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. >> >> :-) mdrun (-: >> >> Option Filename Type Description >> ------------------------------------------------------------ >> -s ethanol.1.tpr Input Run input file: tpr tpb tpa >> -o ethanol.1.trr Output Full precision trajectory: trr trj cpt >> -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) >> -cpi ethanol.1.cpt Input, Opt. Checkpoint file >> -cpo ethanol.1.cpt Output, Opt. Checkpoint file >> -c ethanol.1.gro Output Structure file: gro g96 pdb etc. >> -e ethanol.1.edr Output Energy file >> -g ethanol.1.log Output Log file >> -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file >> -field ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -table ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt >> -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -ei ethanol.1.edi Input, Opt. ED sampling input >> -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -j ethanol.1.gct Input, Opt. General coupling stuff >> -jo ethanol.1.gct Output, Opt. General coupling stuff >> -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -px ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -ra ethanol.1.log Output, Opt. Log file >> -rs ethanol.1.log Output, Opt. Log file >> -rt ethanol.1.log Output, Opt. Log file >> -mtx ethanol.1.mtx Output, Opt. Hessian matrix >> -dn ethanol.1.ndx Output, Opt. Index file >> -multidir ethanol.1 Input, Opt., Mult. Run directory >> -membed ethanol.1.dat Input, Opt. Generic data file >> -mp ethanol.1.top Input, Opt. Topology file >> -mn ethanol.1.ndx Input, Opt. Index file >> >> Option Type Value Description >> ------------------------------------------------------ >> -[no]h bool no Print help info and quit >> -[no]version bool no Print version info and quit >> -nice int 0 Set the nicelevel >> -deffnm string ethanol.1 Set the default filename for all file options >> -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none >> -[no]pd bool no Use particle decompostion >> -dd vector 0 0 0 Domain decomposition grid, 0 is optimize >> -ddorder enum interleave DD node order: interleave, pp_pme or >> cartesian >> -npme int -1 Number of separate nodes to be used for PME, -1 >> is guess >> -nt int 1 Total number of threads to start (0 is guess) >> -ntmpi int 0 Number of thread-MPI threads to start (0 is >> guess) >> -ntomp int 0 Number of OpenMP threads per MPI process/thread >> to start (0 is guess) >> -ntomp_pme int 0 Number of OpenMP threads per MPI process/thread >> to start (0 is -ntomp) >> -pin enum auto Fix threads (or processes) to specific cores: >> auto, on or off >> -pinoffset int 0 The starting logical core number for pinning to >> cores; used to avoid pinning threads from >> different mdrun instances to the same core >> -pinstride int 0 Pinning distance in logical cores for threads, >> use 0 to minimize the number of threads per >> physical core >> -gpu_id string List of GPU id's to use >> -[no]ddcheck bool yes Check for all bonded interactions with DD >> -rdd real 0 The maximum distance for bonded interactions with >> DD (nm), 0 is determine from initial coordinates >> -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate >> -dlb enum auto Dynamic load balancing (with DD): auto, no or yes >> -dds real 0.8 Minimum allowed dlb scaling of the DD cell size >> -gcom int -1 Global communication frequency >> -nb enum auto Calculate non-bonded interactions on: auto, cpu, >> gpu or gpu_cpu >> -[no]tunepme bool yes Optimize PME load between PP/PME nodes or GPU/CPU >> -[no]testverlet bool no Test the Verlet non-bonded scheme >> -[no]v bool no Be loud and noisy >> -[no]compact bool yes Write a compact log file >> -[no]seppot bool no Write separate V and dVdl terms for each >> interaction type and node to the log file(s) >> -pforce real -1 Print all forces larger than this (kJ/mol nm) >> -[no]reprod bool no Try to avoid optimizations that affect binary >> reproducibility >> -cpt real 15 Checkpoint interval (minutes) >> -[no]cpnum bool no Keep and number checkpoint files >> -[no]append bool yes Append to previous output files when continuing >> from checkpoint instead of adding the simulation >> part number to all file names >> -nsteps step -2 Run this number of steps, overrides .mdp file >> option >> -maxh real -1 Terminate after 0.99 times this time (hours) >> -multi int 0 Do multiple simulations in parallel >> -replex int 0 Attempt replica exchange periodically with this >> period (steps) >> -nex int 0 Number of random exchanges to carry out each >> exchange interval (N^3 is one suggestion). -nex >> zero or not specified gives neighbor replica >> exchange. >> -reseed int -1 Seed for replica exchange, -1 is generate a seed >> -[no]ionize bool no Do a simulation including the effect of an X-Ray >> bombardment on your system >> >> >> Back Off! I just backed up ethanol.1.log to ./#ethanol.1.log.1# >> Reading file ethanol.1.tpr, VERSION 4.6.3 (single precision) >> Using 1 MPI thread >> >> starting mdrun 'Ethanol' >> 3000000 steps, 6000.0 ps. >> Segmentation fault >> >> Thank you, >> Chris. >> -- >> gmx-users mailing list gmx-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 list gmx-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 list gmx-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
