Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs
Hi! You may want to try PLUMED, which is the evolution of grometa http://merlino.mi.infn.it/~plumed/PLUMED/Home.html and can do also steered MD and umbrella sampling. Massimiliano On Jan 27, 2010, at 8:48 AM, David van der Spoel wrote: On 1/27/10 7:49 AM, swa...@ncbs.res.in wrote: Dear Dr. Spoel, I am garduate student in National Centre for Biological Sciences(NCBS-TIFR), India. I am willing to do Locally Enhanced Sampling(LES) in one my research project.I saw few webpages on LES using GROMACS but not able to find any proper documentation/tutorial on that. Would you please help me regarding the same?? Thanks, Regards, Please keep questions on the list. Gromacs implements Flooding and Replica Exchange, both are well documented. In addition you can use metadynamics (similar to flooding) with gromacs if you install grometa. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs
Hi, LES as developed by Elber is available in CHARMM and MOIL. Ran. Massimiliano Bonomi wrote: Hi! You may want to try PLUMED, which is the evolution of grometa http://merlino.mi.infn.it/~plumed/PLUMED/Home.html and can do also steered MD and umbrella sampling. Massimiliano On Jan 27, 2010, at 8:48 AM, David van der Spoel wrote: On 1/27/10 7:49 AM, swa...@ncbs.res.in wrote: Dear Dr. Spoel, I am garduate student in National Centre for Biological Sciences(NCBS-TIFR), India. I am willing to do Locally Enhanced Sampling(LES) in one my research project.I saw few webpages on LES using GROMACS but not able to find any proper documentation/tutorial on that. Would you please help me regarding the same?? Thanks, Regards, Please keep questions on the list. Gromacs implements Flooding and Replica Exchange, both are well documented. In addition you can use metadynamics (similar to flooding) with gromacs if you install grometa. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] J-walking REMD
Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this available? Any other thoughts on REMD for large systems are also appreciated. cheers David -- - Dr David Parcej, Goethe Universitat Frankfurt, Institut für Biochemie, Biozentrum N210/1.04, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany - -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with gromacs-openMM
Hi, try to do add the OpenMM library dir to your library path before running make $ export LD_LIBRARY_PATH=/opt/openmm/lib:$LD_LIBRARY_PATH Also, OpenMM support will be officially available in the next Gromacs release (soon). Rossen On 1/27/10 4:28 AM, jorge_quint...@ciencias.uis.edu.co wrote: make[3]: *** No hay ninguna regla para construir el objetivo `/usr/local/openmm/lib/libOpenMM.*', necesario para `grompp'. Alto. make[3]: se sale del directorio `/root/gromacs-4.0.7/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: se sale del directorio `/root/gromacs-4.0.7/src' make[1]: *** [all] Error 2 make[1]: se sale del directorio `/root/gromacs-4.0.7/src' make: *** [all-recursive] Error 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] J-walking REMD
You can try using the TEE-REX module, the GROMACS 3.3.x version has worked for me in the past on a system too large for standard REMD. Tom David Parcej wrote: Dear All Some time ago there was a discussion concerning the problems of REMD for large systems and the possibility of using the REST implementation of the method. Mark, you mentioned that you had coded an implementation Okur method (JCTC, 2006, 2, 420). How did it work and can you make this available? Any other thoughts on REMD for large systems are also appreciated. cheers David -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] linking gromcs to efence
Hi, I am trying to link mdrun with efence, but don't really know how. I have been trying to add the -lefence to the CFLAGS or to the LDFLAGS, but that doesn't seem to work. Any help would be appreciated. Thanks in advance, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] linking gromcs to efence
Hi, Why not use valgrind? I switched from efence to valgrind a long time ago. If you have a Mac it might be less effort to log into a linux machine and run valgrind there. Berk Date: Wed, 27 Jan 2010 17:32:07 +0100 From: joc...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: [gmx-users] linking gromcs to efence Hi, I am trying to link mdrun with efence, but don't really know how. I have been trying to add the -lefence to the CFLAGS or to the LDFLAGS, but that doesn't seem to work. Any help would be appreciated. Thanks in advance, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] linking gromcs to efence
Hi Jochen, it should work by putting it in the LDFLAGS. Either you should then get an executable that says something like Electric Fence 2.2.0 at the very start of execution or it should not compile when the library is not found. Carsten On Jan 27, 2010, at 5:32 PM, Jochen Hub wrote: Hi, I am trying to link mdrun with efence, but don't really know how. I have been trying to add the -lefence to the CFLAGS or to the LDFLAGS, but that doesn't seem to work. Any help would be appreciated. Thanks in advance, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Potential Energy
I did not develop the force field of my molecule by myself. In stead I use the literature force field parameters. I guess not all the force field need the [pairs]. As long as I can get reasonable experimental observables, I can use such force field, right? On Tue, Jan 26, 2010 at 6:50 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Yanmei Song yson...@asu.edu Date: Wednesday, January 27, 2010 10:58 Subject: Re: [gmx-users] Potential Energy To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Dear Justin: I finally figure out that the problem comes from the Coulomb 1-4 interactions defined by [pairs] part. When I remove this parts, the energy minimization ends with a big negative number. Thanks for your help. That's not a solution, that's a random number generator. Whether or not you need such pairs is force-field dependent. Ad hoc changes are ridiculous. Messing with force fields is an expert topic, and parameterizing a new molecule is difficult and risky. 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/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/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs commercial license
Hello folks!! Does anyone know if there is a GROMACS version to commercial use, or under somekind of license? If so, how should I proceed to get such license? Best regards!! -- Att. Guilherme Menegon Giesel -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs commercial license
On Wednesday 27 January 2010 19:40:57 Guilherme Menegon Giesel wrote: Hello folks!! Does anyone know if there is a GROMACS version to commercial use, or under somekind of license? If so, how should I proceed to get such license? Best regards!! Gromacs is under GPLv2 license (http://www.gnu.org/licenses/gpl-2.0.html) and you can use it for commercial purpose without any problem. Milan -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs commercial license
Gromacs is under GPLv2 license (http://www.gnu.org/licenses/gpl-2.0.html) and you can use it for commercial purpose without any problem. EXCEPT distributing new commercial binaries that use any of the Gromacs code, without also distributing the source for the code. (did I get all the GPL correct there? ;) Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Questions about Pull Code
Hello, I am a new Gromacs user, and I could really use some clarification about the pull code. I am interested in creating the PMF for Na+ and I- in the presence of THF. I saw a previous posting that the best way to go about creating the PMF is: 1) Generate a trajectory of configurations along the reaction coordinate. 2) Use the difference configurations as starting points for independent simulations in sampling window. 3) Use umbrella sampling to constrain in window. 4) Use g_wham to construct PMF This is how I am interpreting the instructions, but could you please let me know if I am correct in my assumptions? First I create a couple of unique starting configurations, with Na+ and I- separated by specific distances. Once that has been done, I take one such configuration and turn on the options under com_pulling (especially pull_geometry = umbrella) in the .mdp file. I let this run for some amount of time, and end up with a pullx.xvg and a pullf.xvg file. I do this with the other configurations as well. Once that has been done, I take all of these .xvg and .tpr files and create a .dat file, which can be used with g_wham to construct the PMF. I really appreciate the help. Nobody in my lab has done this before, and I am feeling pretty unsure of myself. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Questions about Pull Code
Jennifer Casey wrote: Hello, I am a new Gromacs user, and I could really use some clarification about the pull code. I am interested in creating the PMF for Na+ and I- in the presence of THF. I saw a previous posting that the best way to go about creating the PMF is: 1) Generate a trajectory of configurations along the reaction coordinate. 2) Use the difference configurations as starting points for independent simulations in sampling window. 3) Use umbrella sampling to constrain in window. 4) Use g_wham to construct PMF This is how I am interpreting the instructions, but could you please let me know if I am correct in my assumptions? First I create a couple of unique starting configurations, with Na+ and I- separated by specific distances. Once that has been done, I take one such configuration and turn on the options under com_pulling (especially pull_geometry = umbrella) in the .mdp file. I let this run for some amount of time, and end up with a pullx.xvg and a pullf.xvg file. I do this with the other configurations as well. Once that has been done, I take all of these .xvg and .tpr files and create a .dat file, which can be used with g_wham to construct the PMF. I really appreciate the help. Nobody in my lab has done this before, and I am feeling pretty unsure of myself. In general, yes, you've got the right procedure. Coincidently, I have just created a PMF/umbrella sampling tutorial that is linked from the Tutorials page on the Gromacs site. The system in the tutorial is certainly more complicated than what you're looking to do, but still might be of use. -Justin Thanks. -- 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/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/mailing_lists/users.php
[gmx-users] Genbox error message
Hello all, Can someone tell me the meaning of this error message after using the genbox command? *** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7e7c454] genbox[0x81195c4] === Memory map: 08048000-082be000 r-xp 08:01 4333977 /usr/local/gromacs/bin/genbox 082be000-082bf000 r-xp 00275000 08:01 4333977 /usr/local/gromacs/bin/genbox 082bf000-082c5000 rwxp 00276000 08:01 4333977 /usr/local/gromacs/bin/genbox 082c5000-082cb000 rwxp 082c5000 00:00 0 0958f000-099e9000 rwxp 0958f000 00:00 0 [heap] b7df3000-b7df4000 rwxp b7df3000 00:00 0 b7df4000-b7e09000 r-xp 08:01 3860700/lib/tls/i686/cmov/ libpthread-2.8.90.so b7e09000-b7e0a000 r-xp 00014000 08:01 3860700/lib/tls/i686/cmov/ libpthread-2.8.90.so b7e0a000-b7e0b000 rwxp 00015000 08:01 3860700/lib/tls/i686/cmov/ libpthread-2.8.90.so Aborted I appreciate your help. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Genbox error message
On 28/01/10 13:06, Lum Nforbi wrote: Hello all, Can someone tell me the meaning of this error message after using the genbox command? Certainly not without more useful information - GROMACS version, simulation system size, actual command line. Even then, the best guess is probably that you're running genbox on a machine for which it wasn't compiled, or for which some shared libraries have been updated in an incompatible way. Try recompiling GROMACS if so. Mark *** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7e7c454] genbox[0x81195c4] === Memory map: 08048000-082be000 r-xp 08:01 4333977 /usr/local/gromacs/bin/genbox 082be000-082bf000 r-xp 00275000 08:01 4333977 /usr/local/gromacs/bin/genbox 082bf000-082c5000 rwxp 00276000 08:01 4333977 /usr/local/gromacs/bin/genbox 082c5000-082cb000 rwxp 082c5000 00:00 0 0958f000-099e9000 rwxp 0958f000 00:00 0 [heap] b7df3000-b7df4000 rwxp b7df3000 00:00 0 b7df4000-b7e09000 r-xp 08:01 3860700 /lib/tls/i686/cmov/libpthread-2.8.90.so http://libpthread-2.8.90.so b7e09000-b7e0a000 r-xp 00014000 08:01 3860700 /lib/tls/i686/cmov/libpthread-2.8.90.so http://libpthread-2.8.90.so b7e0a000-b7e0b000 rwxp 00015000 08:01 3860700 /lib/tls/i686/cmov/libpthread-2.8.90.so http://libpthread-2.8.90.so Aborted I appreciate your help. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
