- Tremolo-users - Mailman3

Problem with Brenner
by Rogers, Daniel J 04 Dec '08

04 Dec '08

Hello, Cannot run simulation with Brenner Potential (tube example). I receive the following error message: error: in ../src/parser.c:642: parse error in .potentials:5:7 (col 7): unknown symbol I cannot run successfully with Brenner on a custom simulation either. Does anyone have a test case I could use to trouble Brenner? Any idea with this error? Thanks, Dan

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Tremolo GUI
by Rogers, Daniel J 04 Dec '08

04 Dec '08

What command line is used to launch the GUI? Thanks,Dan

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Tremolo Bug
by Rogers, Daniel J 03 Dec '08

03 Dec '08

Greetings, I am a new user of TREMOLO. Upon using the 'make check' command I receive the following to errors indicating that 2/3 tests have failed. I can run the h20 example successful, however the tube example fails. What is causing this test failure? Thank you for your help, Daniel J Rogers Georgia Institute of Technology -------------------- make check-TESTS make[2]: Entering directory `/home/drogers/TREMOLO/2008/tests' File is open: argon.tremolo project comment: Argon example in ./init.c:129: parse warning in .tremolo:4:28 (col 28): custom system of units not yet implemented mainpath:./ mainname:argon Reading simulation parameters: argon Default path is /home/drogers/TREMOLO/2008/defaults/argon/argon File is open: argon.validates error: in ./parser.c:623: parse error in .validates:2:14 (col 21): undefined state in state machine reached FAIL: example.test project comment: Argon example in ../src/init.c:129: parse warning in .tremolo:4:28 (col 28): custom system of units not yet implemented error: in ../src/parser.c:623: parse error in .validates:2:14 (col 21): undefined state in state machine reached [cluster.georgiatech-metz.fr:10327] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1 FAIL: example.2.test --------------------

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[Fwd: RE: Compilation Problem solved]
by Tim Golla 03 Sep '08

03 Sep '08

-------- Original-Nachricht -------- Betreff: RE: Compilation Problem solved Datum: Wed, 3 Sep 2008 09:27:35 +0200 Von: Seybold Hansjörg <seybold(a)ifb.baug.ethz.ch> An: Tim Golla <golla(a)ins.uni-bonn.de> Referenzen: <20080902115558.GA14063(a)ins.uni-bonn.de> <48BD822A.3060502(a)ins.uni-bonn.de> <A55C511E22AF004FB95FBCE3E3B8DFB401D72B20(a)EX2.d.ethz.ch> <48BD8EB7.5080903(a)ins.uni-bonn.de> Hello! I found the error. The problem was that the configure found a qt3 installation, but did not use the corresponding moc to compile the code, so it tried to compile with the qt4 version. after changing all makefiles to the right path i succeeded to compile the gui. Here the complete discription of the changes (for the mailing list) ------------------------------------------------------------------------------------------------ - on suse 10.3(x64) qt3 is installed in /usr/lib64/qt3, binaries are under /usr/lib64/qt3/bin/ - the configure file finds the qt3 path but does not include the qt3 binary path. - Chgange the Makefile, src/Makefile, (doc/Makefile) and replace the line MOC = /bin/moc with MOC = /usr/lib64/qt3/bin/moc if you have qt3 installed in another path modify the line accordingly. then make compiles the guy ------------------------------------------------------------------------------------------------ Sorry for the inconvenience and thanks a lot for the help. It would be nice to keep me up to date about the new version of tremolo. best hansjoerg -----Original Message----- From: Tim Golla [mailto:golla@ins.uni-bonn.de] Sent: Tue 9/2/2008 9:06 PM To: Seybold Hansjörg Cc: tremolo-users(a)ins.uni-bonn.de Subject: Re: Compilation Problem Hi Hansjörg, could you send me the output generated by the TremoloGUI configure script? Are you able to compile other programs using Qt3? Regards, Tim Seybold Hansjörg schrieb: > thanks a lot for the answer > I tried to subscribe, but I think somethign went wrong, so i'll try again, > I am using QT3 (3.3) on suse linux 10.3 x64, gcc version 4.2.3 20071030 (prerelease) (SUSE Linux), hope this helps > to find the clue. > > I also tried on an older machine with suse 10.0 and gcc version 4.0.2 20050901 (prerelease) (SUSE Linux) > but with the same problem. > > It would be kind to remind me when you release a new version. > Thanks a lot for the info > best hansjoerg > > > > > -----Original Message----- > From: Tim Golla [mailto:golla@ins.uni-bonn.de] > Sent: Tue 9/2/2008 8:12 PM > To: Seybold Hansjörg > Cc: Ralf Wildenhues > Subject: Re: [Fwd: FW:] > > Hi, > > could you give us some details concerning your configuration? Which > Linux distribution (or Cygwin?) are you using? > > Tim > >> ------------------------------------------------------------------------ >> >> Betreff: >> FW: >> Von: >> Seybold Hansjörg <seybold(a)ifb.baug.ethz.ch> >> Datum: >> Tue, 2 Sep 2008 12:04:08 +0200 >> An: >> <mol(a)ins.uni-bonn.de> >> >> An: >> <mol(a)ins.uni-bonn.de> >> >> >> Hi! >> I tried to post my question on the user list, but I don't know if it arrived there. >> Hope you can help me. >> thanks a lot hansjoerg >> >> -----Original Message----- >> From: Seybold Hansjörg >> Sent: Fri 8/29/2008 11:05 AM >> To: tremolo-users(a)ins.uni-bonn.de >> Subject: >> >> Hi! >> I am new on the tremolo list and i'd like to try out the MD code. >> I successfully downloaded the tremolo-0.5.tar.gz package and compiled it successfully with MPI support. >> The make check runs through the help test but fails for the other two. >> testing the serial code with the examples in tremolo-0.5/defaults fails when parsing the file >> e.g. for the h2o example >> =============================================================================================== >> ... >> You have: kcal / mole N_A angstrom^3 >> You want: bar >> * 69523.497 >> / 1.4383626e-05 >> >> >> in ./parse.c:238: parse warning in .validates:4:43 (col 43): Ignoring validation of force_type >> in ./parse.c:238: parse warning in .validates:5:35 (col 35): Ignoring validation of force_type >> in ./parse.c:238: parse warning in .validates:6:36 (col 36): Ignoring validation of force_type >> in ./parser.c:460: parse warning in .potentials:2:158 (col 190): reading integer as double >> in ./parser.c:460: parse warning in .potentials:3:158 (col 190): reading integer as double >> Keyword combination unknown: 2 keys: angle spme >> error: in ./parser.c:387: parse error in .parameters:65:24 (col 46): unknown symbol >> ================================================================================================ >> Other examples fail due to similar reasons when parsing the files. >> Is there a new version 0.6? and the examples already ise some new keys? >> >> In particular i'd like to try out the gui version, but i was not able to compile either the tremologui-0.6.tar.gz >> or the tremologui-0.5.tar.gz >> >> * configure works fine >> * make falis with the errors >> ================================================================================================ >> ... >> In file included from angletable.cpp:353: >> angletable.moc:11:2: error: #error "The header file 'angletable.h' doesn't include <QObject>." >> In file included from angletable.cpp:353: >> angletable.moc:60: error: 'const QMetaObject AngleTable::staticMetaObject' is not a static member of 'class AngleTable' >> angletable.moc:60: error: variable 'const QMetaObject AngleTable::staticMetaObject' has initializer but incomplete type >> angletable.moc:65: error: prototype for 'const QMetaObject* AngleTable::metaObject() const' does not match any in class 'AngleTable' >> angletable.h:33: error: candidate is: virtual QMetaObject* AngleTable::metaObject() const >> angletable.moc:65: error: 'const QMetaObject* AngleTable::metaObject() const' cannot be overloaded >> ... >> ================================================================================================== >> perhaps you can give me some hints how i can get the gui running. >> >> thanks a lot hansjoerg >> >> >> >> >> >> >> >> >> > > > >

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Re: [Tremolo-users] Compilation Problem
by Tim Golla 02 Sep '08

02 Sep '08

Hi Hansjörg, could you send me the output generated by the TremoloGUI configure script? Are you able to compile other programs using Qt3? Regards, Tim Seybold Hansjörg schrieb: > thanks a lot for the answer > I tried to subscribe, but I think somethign went wrong, so i'll try again, > I am using QT3 (3.3) on suse linux 10.3 x64, gcc version 4.2.3 20071030 (prerelease) (SUSE Linux), hope this helps > to find the clue. > > I also tried on an older machine with suse 10.0 and gcc version 4.0.2 20050901 (prerelease) (SUSE Linux) > but with the same problem. > > It would be kind to remind me when you release a new version. > Thanks a lot for the info > best hansjoerg > > > > > -----Original Message----- > From: Tim Golla [mailto:golla@ins.uni-bonn.de] > Sent: Tue 9/2/2008 8:12 PM > To: Seybold Hansjörg > Cc: Ralf Wildenhues > Subject: Re: [Fwd: FW:] > > Hi, > > could you give us some details concerning your configuration? Which > Linux distribution (or Cygwin?) are you using? > > Tim > >> ------------------------------------------------------------------------ >> >> Betreff: >> FW: >> Von: >> Seybold Hansjörg <seybold(a)ifb.baug.ethz.ch> >> Datum: >> Tue, 2 Sep 2008 12:04:08 +0200 >> An: >> <mol(a)ins.uni-bonn.de> >> >> An: >> <mol(a)ins.uni-bonn.de> >> >> >> Hi! >> I tried to post my question on the user list, but I don't know if it arrived there. >> Hope you can help me. >> thanks a lot hansjoerg >> >> -----Original Message----- >> From: Seybold Hansjörg >> Sent: Fri 8/29/2008 11:05 AM >> To: tremolo-users(a)ins.uni-bonn.de >> Subject: >> >> Hi! >> I am new on the tremolo list and i'd like to try out the MD code. >> I successfully downloaded the tremolo-0.5.tar.gz package and compiled it successfully with MPI support. >> The make check runs through the help test but fails for the other two. >> testing the serial code with the examples in tremolo-0.5/defaults fails when parsing the file >> e.g. for the h2o example >> =============================================================================================== >> ... >> You have: kcal / mole N_A angstrom^3 >> You want: bar >> * 69523.497 >> / 1.4383626e-05 >> >> >> in ./parse.c:238: parse warning in .validates:4:43 (col 43): Ignoring validation of force_type >> in ./parse.c:238: parse warning in .validates:5:35 (col 35): Ignoring validation of force_type >> in ./parse.c:238: parse warning in .validates:6:36 (col 36): Ignoring validation of force_type >> in ./parser.c:460: parse warning in .potentials:2:158 (col 190): reading integer as double >> in ./parser.c:460: parse warning in .potentials:3:158 (col 190): reading integer as double >> Keyword combination unknown: 2 keys: angle spme >> error: in ./parser.c:387: parse error in .parameters:65:24 (col 46): unknown symbol >> ================================================================================================ >> Other examples fail due to similar reasons when parsing the files. >> Is there a new version 0.6? and the examples already ise some new keys? >> >> In particular i'd like to try out the gui version, but i was not able to compile either the tremologui-0.6.tar.gz >> or the tremologui-0.5.tar.gz >> >> * configure works fine >> * make falis with the errors >> ================================================================================================ >> ... >> In file included from angletable.cpp:353: >> angletable.moc:11:2: error: #error "The header file 'angletable.h' doesn't include <QObject>." >> In file included from angletable.cpp:353: >> angletable.moc:60: error: 'const QMetaObject AngleTable::staticMetaObject' is not a static member of 'class AngleTable' >> angletable.moc:60: error: variable 'const QMetaObject AngleTable::staticMetaObject' has initializer but incomplete type >> angletable.moc:65: error: prototype for 'const QMetaObject* AngleTable::metaObject() const' does not match any in class 'AngleTable' >> angletable.h:33: error: candidate is: virtual QMetaObject* AngleTable::metaObject() const >> angletable.moc:65: error: 'const QMetaObject* AngleTable::metaObject() const' cannot be overloaded >> ... >> ================================================================================================== >> perhaps you can give me some hints how i can get the gui running. >> >> thanks a lot hansjoerg >> >> >> >> >> >> >> >> >> > > > >

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Re: [Tremolo-users] Tremolo- little guidance required
by Ralf Wildenhues 05 May '08

05 May '08

Hello Nayyar, * Nayyar Afaq wrote on Sat, May 03, 2008 at 09:36:14AM CEST: > > Hope you would be fine. I have just googled up "Tremolo", and dont know much > about the performance of it. Please, guide me about the given; > > 1- Is Tremolo functionable in Windows? If not, please guide in which > version of Linux it functions well? It should work on both Windows and Linux, and all sorts of unices. On Windows, please install Cygwin and its FFTW and MPI packages prior to building Tremolo. Please report any build issues you encounter, so we can fix them. > 2- I want to get simulation study of mechanical properties of a Protein > structure. Is Tremolo a good choice for it, i.e., Does Tremolo consider all > the required interactions, like bonded, non-bonded, hydrogen bonding > interactions, disulphide, salt bridge, etc. With Tremolo, you have to list all bonded interactions explicitly, esp. the hydrogen bonds, and disulphide and salt bridges. Typically this can be done easily with a preparatory script (we have one but it's not fully general, so it may need to be adjusted for the input). This might require some small programming efforts. Non-bonded interactions are handled as usual: excluded within the first three bonded neighbors, and possibly scaled for the 1-4 neighbor. > 3- Is Tremolo easy to understand and use. Infact, I have no skill of > programming, and I prefer to work in user friendly graphical interface? There is a graphical user interface that allows to adjust most settings, but the atomic coordinates and connection data are so far read in via a file only. Also, there is unfortunately no extensive user manual yet. Regards, Ralf -- Ralf Wildenhues University of Bonn, Department of Numerical Simulation Wegelerstrasse 6, 53115 Bonn, Germany tel: +49 228 733178 mailto:wildenhues@ins.uni-bonn.de fax: +49 228 737527 http://wissrech.ins.uni-bonn.de/people/wildenhues.html

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version 0.6 404
by Charles Radeke 03 Apr '08

03 Apr '08

Dear Tremolos! I'm glad to join the list. We are ongoing to look into tremolo to see if we can do scientific with it efficiently. The tremolo-0.6 download link is dead. Should we start with version 0.5? C. Radeke Research associate Rutgers, the State University of New Jersey CBE, 98 Brett Rd, 08854 Piscataway -- Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! http://games.entertainment.gmx.net/de/entertainment/games/free

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Re: [Tremolo-users] Stress-strain questions
by caoch 20 Feb '08

20 Feb '08

Dear Ralf Thank you for the answer. Please inform me when you put a Non- equilibration example in the tar file. At this time, Can you tell the way of setting an external stress tensor in the simulation parameter file? For example, if I want to add 0.01Gpa/ps external stress along the second axis, say Y direction, how can I set time step(1ps), tensor(the value of XX YY ZZ XY XZ YZ) and the real stress(0.01Gpa)? Although I think these setup should be easily defined in the ensemble and propagator section of the simulation parameter file, I don't know what these keywords are. Furthermore, is it possible for setting a limitation value to the simulation system, such as the simulation will be stopped when the loaded strain reached to some value? Best regards ---------------------------- Caoch JST-CREST Researcher Fundamental Technology Laboratory Research and Development Division Mitsubishi Chemical Group Science and Technology Research Center, INC. 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan TEL +81-45-963-3264 caoch(a)rsi.co.jp ---------------------------- -----Original Message----- From: Ralf Wildenhues [mailto:wildenhues@ins.uni-bonn.de] Sent: Tuesday, February 19, 2008 6:30 PM To: caoch Cc: tremolo-users(a)ins.uni-bonn.de Subject: Re: [Tremolo-users] Stress-strain questions Dear Caoch, * caoch wrote on Tue, Feb 19, 2008 at 08:15:05AM CET: > > I have some questions for the simulation run. Thanks for your interest in Tremolo. We have made a package available, but not yet announced it, because there are a few known issues we'd like to still fix first. Announcement and updated package are to follow real soon now. > 1) According to the above paper, such simulation should be done by add > a tensile load with a stress rate. I think this is a Non-equilibration MD > approach. However, the simulation parameters file seems only allow > equilibration setting. How can I define these parameters into the simulation > parameters file? I'll make sure there is a non-equilibration example in the tree, and at least a bit of documentation for the add-on tools. > 4) Is there a complete manual of Tremolo? Because I want to understand > the properties of the program (including calculation algorithms, results > analysis tools and so or) absolutely. At this time, such a thing does not exist, unfortunately. Most algorithmic details are explained in the published book, and we're working on a docbook-style document for the simulation code. Best regards, Ralf -- Ralf Wildenhues University of Bonn, Department of Numerical Simulation Wegelerstrasse 6, 53115 Bonn, Germany tel: +49 228 733178 mailto:wildenhues@ins.uni-bonn.de fax: +49 228 737527 http://wissrech.ins.uni-bonn.de/people/wildenhues.html

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Stress-strain questions
by caoch 19 Feb '08

19 Feb '08

Dear Tremolo developers; Thank you for opening the Tremolo MD source. I have downloaded the source code and want to do some simulations for predicting the elastic moduli of polymer. Such simulation is very similar with the work you published at INS preprint No 0503 (Molecular dynamics simulations of the influence of chemical cross-links on the elastic moduli of polymer-carbon nanotube composites). I have some questions for the simulation run. 1) According to the above paper, such simulation should be done by add a tensile load with a stress rate. I think this is a Non-equilibration MD approach. However, the simulation parameters file seems only allow equilibration setting. How can I define these parameters into the simulation parameters file? 2) According to the application tools introduction on the website. It seems there is a tool, which can be used for plot stress-strain relationship, in the Tremolo. Can you tell me which is the tool is and how to use this tool? 3) Can you send me one example file for doing stress-strain simulation, such as you did in the above paper? Because I also want to check some benchmark properties of Tremolo? 4) Is there a complete manual of Tremolo? Because I want to understand the properties of the program (including calculation algorithms, results analysis tools and so or) absolutely. Best regards ---------------------------- Caoch JST-CREST Researcher Fundamental Technology Laboratory Research and Development Division Mitsubishi Chemical Group Science and Technology Research Center, INC. 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-8502, Japan TEL +81-45-963-3264 caoch(a)rsi.co.jp ----------------------------

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