Re: [gmx-users] dssp and gromacs version
On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Ha ... the dssp complain the segmentation fault in 4.5.5, but can run smoothly in 4.5.3. IIRC, seems there were some threads talked about that before. Mark -- 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 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] dssp and gromacs version
Gromacs' 4.5.5 do_dssp is broken. There is a patch for it in git. I haven't tried it out, so I can't say for sure it works. This is not a DSSP problem, it's a Gromacs problem. Just to reinforce the idea, the new DSSP should not be used, no matter which Gromacs version you're using. Best regards, Joao Henriques On Fri, Mar 2, 2012 at 9:10 AM, lina lina.lastn...@gmail.com wrote: On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Ha ... the dssp complain the segmentation fault in 4.5.5, but can run smoothly in 4.5.3. IIRC, seems there were some threads talked about that before. 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 -- João Henriques -- 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] MDrun append...
Dear Rama, Since the latest version, I have to use -noappend and then just concantenate them when they are finished. I gave up as no mater how many paths to files, listening to the error messages, I supplied to the mdrun it still complained. Dont know if this is a personalized bug or more general, but figured the former and was not such a big deal, so never wrote here. Stephan Original-Nachricht Datum: Fri, 02 Mar 2012 17:31:49 +1100 Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] MDrun append... On 2/03/2012 3:59 PM, rama david wrote: Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called 'traj.trr' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend What to do ??? Update whichever of your filesystem or mdrun is outdated, or use -noappend and resign yourself to concatenation after the simulation completes. 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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] Gromacs-GPU benchmark test killed after exhausting the memory
Hi, First I thought that there might be a memory leak which could have caused this if you ran for really long time. However, I've just ran the very same benchmark (dhfr with PME) for one hour, monitored the memory usage and I couldn't see any change whatsoever (see the plot attached). I've attached a script I used to monitor the memory usage, feel free to use if you want check again. Cheers, -- Szilárd On Wed, Feb 29, 2012 at 9:50 AM, Efrat Exlrod efrat.exl...@biu.ac.il wrote: Hi, I have Gromacs-GPU version 4.5.5 and GTX 580. I ran dhfr-solv-PME benchmark test (see below) and my run was killed after couple of hours exhausting all the computer memory, including the swap (2G + 4G swap). Has anyone encountered this problem? What is wrong? Thanks, Efrat mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -deffnm md :-) G R O M A C S (-: Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.5.5 (-: 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-gpu (-: Option Filename Type Description -s md.tpr Input Run input file: tpr tpb tpa -o md.trr Output Full precision trajectory: trr trj cpt -x md.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi md.cpt Input, Opt. Checkpoint file -cpo md.cpt Output, Opt. Checkpoint file -c md.gro Output Structure file: gro g96 pdb etc. -e md.edr Output Energy file -g md.log Output Log file -dhdlmd.xvg Output, Opt. xvgr/xmgr file -field md.xvg Output, Opt. xvgr/xmgr file -table md.xvg Input, Opt. xvgr/xmgr file -tablep md.xvg Input, Opt. xvgr/xmgr file -tableb md.xvg Input, Opt. xvgr/xmgr file -rerun md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi md.xvg Output, Opt. xvgr/xmgr file -tpidmd.xvg Output, Opt. xvgr/xmgr file -ei md.edi Input, Opt. ED sampling input -eo md.edo Output, Opt. ED sampling output -j md.gct Input, Opt. General coupling stuff -jo md.gct Output, Opt. General coupling stuff -ffout md.xvg Output, Opt. xvgr/xmgr file -devout md.xvg Output, Opt. xvgr/xmgr file -runav md.xvg Output, Opt. xvgr/xmgr file -px md.xvg Output, Opt. xvgr/xmgr file -pf md.xvg Output, Opt. xvgr/xmgr file -mtx md.mtx Output, Opt. Hessian matrix -dn md.ndx Output, Opt. Index file -multidirmd Input, Opt., Mult. Run directory Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint 0 Set the nicelevel -deffnm string md 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 -npmeint -1 Number of separate nodes to be used for PME, -1 is guess -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -[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 -gcomint -1 Global communication frequency -[no]v bool no
Re: [gmx-users] impropers and residue number
Lara Bunte wrote: Hello I got this error: Fatal error: Atom ON1 is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 1. What do this mean? How to fix it? The Atom ON1 is declared in atomtypes.atp file. In my .rtp file I used [ impropers ] and I use a charmm27 force field. Impropers are specified in the .rtp file by atom name, not type. So the error indicates that pdb2gmx (?) thinks an atom *named* ON1 should be present, which it is not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Lennard-Jones Interactions in Gromacs
Hi In a supporting Information of a paper is written: The description of the LF radical force fields is complete, as soon as also the parameters of the Lennard-Jones potentials are given. For these parameters we adopt the values specified in the CHARMM22 force field for the basic atom types Please tell me how, what and where I have to do this. I know that Lennard-jones interactions are in the ffnonbonded.itp file in the section [ pairtypes ]but I don't know what to do. Sorry for my probably stupid question but I don't understand it. :-( Thank you very much for your help. Greetings Lara -- 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] Re: Re: mdrun -multi flag (Mark Abraham)
Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Bo On Thu, Mar 1, 2012 at 7:42 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: mdrun -multi flag (Mark Abraham) 2. Re: dihedral distributions (Juliette N.) -- Message: 1 Date: Fri, 02 Mar 2012 10:17:12 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] mdrun -multi flag To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4f500378.7030...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/03/2012 10:15 AM, bo.shuang wrote: Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Then I tried re-install mdrun: ./configure --enable-mpi --program-suffix=_mpiq make mdrun make install-mdrun It looks fine, but I still cannot use multi flag, and it is still the same error. I don't know what the problem is and what I should do next. Thank you for help! With that program suffix, you need to use mdrun_mpiq Mark -- Message: 2 Date: Thu, 1 Mar 2012 20:42:06 -0500 From: Juliette N. joojoojo...@gmail.com Subject: Re: [gmx-users] dihedral distributions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cagdqh4os1kuuogwlncznyxrf9sra_+a8s0eku2bum6cojvz...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Skipped content of type multipart/alternative-- next part -- A non-text attachment was scrubbed... Name: RB1.88.PNG Type: image/png Size: 9359 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20120301/e812dbaf/RB1.88.png -- next part -- A non-text attachment was scrubbed... Name: RB1.46.PNG Type: image/png Size: 9580 bytes Desc: not available Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20120301/e812dbaf/RB1.46.png -- -- 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! End of gmx-users Digest, Vol 95, Issue 10 * -- 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] Re: Re: mdrun -multi flag (Mark Abraham)
bo.shuang wrote: Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Running multiple simulations requires multiple processors. For 2 simulations, you need at least 2 processors (one for each simulation). More can be used, but it must be a multiple of the number of simulations, as the error message indicates. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Extending simulation with -pd
On 2012-03-02 05:25:01PM +, Steven Neumann wrote: Dear Gmx Users, I run nvt simulation with small timestep with implicit solvent for 500 ps. I used particle decomposition for this run (-pd). No I want to extend my simulation with different mdp file from the previous nvt using: grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt mdrun -s new.tpr (-pd?) This is my question - shall use -pd option again or will it be considered automatically? The manual entry for mdrun tells you what commandline switches are considered enabled by default. I don't think -pd is one of them so you will have to specify it every time (it's safer to specify it anyway). -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] [ bondedtypes ]
Hi The first part in a .rtp file is the [ bondedtypes ] with syntax [ bondedtypes ] ; bonds angles dihedrals impropers 1 1 1 2 1.) What do this numbers mean? I found nothing in the manual to that. 2.) If you have improper dihedrals, do you really nead both in this section? Why not only impropers? Thanks Greetings -- 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] Re: Lennard-Jones Interactions in Gromacs
Please help :-( Greetings Lara -- 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] Re: Lennard-Jones Interactions in Gromacs
Lara Bunte wrote: Please help :-( Please realize that you're asking for free help from a global mailing list. You may not get a reply from someone immediately, as that person may be busy with their own work, or even asleep ;) From your original post: In a supporting Information of a paper is written: The description of the LF radical force fields is complete, as soon as also the parameters of the Lennard-Jones potentials are given. For these parameters we adopt the values specified in the CHARMM22 force field for the basic atom types Please tell me how, what and where I have to do this. I know that Lennard-jones interactions are in the ffnonbonded.itp file in the section [ pairtypes ]but I don't know what The [pairtypes] directive is for adding special 1-4 interactions. Everything else is simply stated in the [atomtypes] directive, providing sigma/epsilon or C6/C12 parameters, whatever is required by the force field. L-J interactions between different atom types are then generated according to combination rules. Some force fields (like Gromos) use additional [nonbond_params] for interactions that do not follow standard combination rules, but that's not necessarily relevant here. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] [ bondedtypes ]
Lara Bunte wrote: Hi The first part in a .rtp file is the [ bondedtypes ] with syntax [ bondedtypes ] ; bondsanglesdihedralsimpropers 1 1 1 2 1.) What do this numbers mean? I found nothing in the manual to that. They are the function types for these different interactions. Function types are listed in Table 5.5. 2.) If you have improper dihedrals, do you really nead both in this section? Why not only impropers? The order of the function types must be adhered to so that the parameters are properly interpreted. Check gmx.ff/aminoacids.rtp for a complete description of each of the 8 possible columns and the order that they must follow. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul)
Thank you for help! Is that possible to run REMD on a PC with only one processor? Bo bo.shuang wrote: Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Running multiple simulations requires multiple processors. For 2 simulations, you need at least 2 processors (one for each simulation). More can be used, but it must be a multiple of the number of simulations, as the error message indicates. -Justin -- 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] [ bondedtypes ]
On 3/03/2012 5:17 AM, Lara Bunte wrote: Hi The first part in a .rtp file is the [ bondedtypes ] with syntax [ bondedtypes ] ; bondsanglesdihedralsimpropers 1 1 1 2 1.) What do this numbers mean? I found nothing in the manual to that. Manual 5.6.1 - title residue database. Mark 2.) If you have improper dihedrals, do you really nead both in this section? Why not only impropers? Thanks Greetings -- 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] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul)
On 3/03/2012 7:34 AM, bo.shuang wrote: Thank you for help! Is that possible to run REMD on a PC with only one processor? No. See http://www.gromacs.org/Documentation/How-tos/REMD Mark Bo bo.shuang wrote: Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Running multiple simulations requires multiple processors. For 2 simulations, you need at least 2 processors (one for each simulation). More can be used, but it must be a multiple of the number of simulations, as the error message indicates. -Justin -- 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] Anomalous temperature
Dear gmx users, It seems that I have found a strange temperature value after NVT equilibrium for 200 ps. I simulate a CNT with two graphite sheets in water box. I do not want to them to deform or change their shaps, So I use a very large position restraint (1*10^6) to keep their shaps. The temperature was set to 300 K, but after NVT equilibrium, the tempertaure was 330K. .mdp content define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 1 ; Groups to couple separately tc-grps = Other Water_and_ions ; Time constant (ps) and reference temperature (K) tau-t = 0.1 0.1 ref-t = 300 300 results Energy Average Err.Est. RMSD Tot-Drift --- Temperature 331.548 2.6 10.3739 15.0042 (K) T-Other 436.927 12 39.4112 67.2519 (K) T-Water_and_ions 303.349 0.16 6.07417 1.02328 (K) the Other, that is CNT and two graphite sheets temperature is very high!!! Howerver when I freeze them, the temperture is OK freezegrps = K CL Other freezedim = Y Y Y Y Y Y Y Y Y the results is Energy Average Err.Est. RMSD Tot-Drift --- Temperature 299.998 0.0034 4.84173 -0.0066645 (K) T-Other 0 0 0 0 (K) T-Water_and_ions 299.998 0.0034 4.84173 -0.0066645 (K) So I should freeze them or use a small postion restraint to constaint them, in order to get the correct temperture? Zhongjin He-- 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] do_dssp segmentation fault
Dear all, Iam trying to generate secondary structure plot through do_dssp program, but there was an error like segmentation fault Reading file md.tpr, VERSION 4.0.7 (single precision) Reading file md.tpr, VERSION 4.0.7 (single precision) Segmentation fault (core dumped) bash-4.1# can anybody please say what it means and how to solve it Regards, -- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210 -- 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] do_dssp segmentation fault
On 3/03/2012 5:14 PM, arun kumar wrote: Dear all, Iam trying to generate secondary structure plot through do_dssp program, but there was an error like segmentation fault Reading file md.tpr, VERSION 4.0.7 (single precision) Reading file md.tpr, VERSION 4.0.7 (single precision) Segmentation fault (core dumped) bash-4.1# can anybody please say what it means and how to solve it No, because there's no diagnostic information. Do other GROMACS tools work? Does the DSSP executable work? 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
Re: [gmx-users] Anomalous temperature
On 3/03/2012 5:08 PM, zhongjin wrote: Dear gmx users, It seems that I have found a strange temperature value after NVT equilibrium for 200 ps. I simulate a CNT with two graphite sheets in water box. I do not want to them to deform or change their shaps, So I use a very large position restraint (1*10^6) to keep their shaps. The temperature was set to 300 K, but after NVT equilibrium, the tempertaure was 330K. .mdp content define = -DPOSRES_CNTGATE -DPOSRES_K -DPOSRES_CL ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 1 ; Groups to couple separately tc-grps = Other Water_and_ions ; Time constant (ps) and reference temperature (K) tau-t= 0.1 0.1 ref-t= 300 300 results Energy Average Err.Est. RMSD Tot-Drift --- Temperature 331.5482.610.373915.0042 (K) T-Other 436.927 1239.411267.2519 (K) T-Water_and_ions303.349 0.166.074171.02328 (K) the Other, that is CNT and two graphite sheets temperature is very high!!! Howerver when I freeze them, the temperture is OK freezegrps = K CL Other freezedim= Y Y Y Y Y Y Y Y Y the results is Energy Average Err.Est. RMSD Tot-Drift --- Temperature 299.998 0.00344.84173 -0.0066645 (K) T-Other 0 0 0 0 (K) T-Water_and_ions299.998 0.00344.84173 -0.0066645 (K) So I should freeze them or use a small postion restraint to constaint them, in order to get the correct temperture? By introducing position restraints, you cause local heating because there is a force whenever the positions deviate. Don't try to measure local temperature until the model might make a sensible measurement, i.e. after equilibration. That might mean several equilibration phases where you relax your position restraints gradually. The thin nature of the sheet and tube is also somewhat unfavorable for the correct function of separate T-coupling groups. See manual 3.4.8, particularly final subsection and ref therein. 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
