Re: [gmx-users] CPMD- QM MM simulation
Message: 1 Date: Fri, 5 Sep 2008 15:48:12 -0700 From: Chih-Ying Lin [EMAIL PROTECTED] Subject: [gmx-users] CPMD- QM MM simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi I read some papers, which the authors use CPMD - QM MM simulation to reparametrize the force field parameters. But, they did not say the details. Could anyone explain this more here? Why don't you contact the authors? Gerrit ___ 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: trr file format
gurgo Vitaly Chaban wrote: Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Thanks. gurgo Make your life easier by just using the supplied functions to read the gurgo files. Check any analysis program. Thank you very much. Initially I supposed to write my trajectory analysis programme not in C (and thereby wanted to read trajectory from my programme) but after your suggestion and looking into the deeply hidden functions in gromacs I comply to code it in C using the already existing tools.:) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] Software for ESP fitting
Vasilii Artyukhov wrote: Hi gmx-users, Sorry for a not-strictly-GROMACS-related question, but could someone suggest a program I could use to fit atomic charges to quantum chemistry results? antechamber. Thanks in advance, Vasilii ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Fatel error in simulated annealing
ravi sharma wrote: Thanks justin, but how can identify these groups, i am using fedora core 8, also Thanks for the Tc-grps, What groups are you talking about, tc-grps? Please be more specific. -Justin regards, --- On *Sun, 7/9/08, Justin A. Lemkul /[EMAIL PROTECTED]/* wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Fatel error in simulated annealing To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sunday, 7 September, 2008, 10:28 PM You have trailing characters in your simulated annealing section: What shows up for me is: ;simulated annealing annealing = single^M annealing_npoints = 5 ^M annealing_time = 2 500 1000 1500 2000^M annealing_temp = 300 350 400 450 450^M Are you transferring between Windows and Linux/Mac/etc. systems? If so, you will need to process your .mdp file with dos2unix. Unsolicited advice on T-coupling: tc-grps = Protein SOL HEM NA+ It's a bad idea to couple solvent, ions, and small molecules all in different tc-grps. Reference here for information regarding thermostats: http://wiki.gromacs.org/index.php/thermostats -Justin ravi sharma wrote: Hello guys, i am doing a simulation with simulated annealing of a protein which contains heme inside, the normal without simulated annealing its running fine but while m writing simulated annealing in my md.mdp its showing error //Fatal error: Not enough annealing values: 1 (for 4 groups) http://www.gromacs.org/mailman/listinfo/gmx-users// I am attaching my md.mdp file here md.mdp Thanks Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On *Sun, 7/9/08, Florian Dommert /[EMAIL PROTECTED]/* wrote: From: Florian Dommert [EMAIL PROTECTED] Subject: Re: [gmx-users] trr file format To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sunday, 7 September, 2008, 4:54 PM On 06.09.2008, at 22:28, Vitaly Chaban wrote: Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Hello, if you have problems, finding appropiate header files for the functions of gmx, you can perhaps use a development environment like Eclipse, Source-Navigator, KDevelop, Anjuta depending on your flavour and operating system. This programs index all the functions in a specified project and you can look up their definitions by request without searching the files of the complete src-code. It is hard to rank the different programs due to their various capabilities and your requirements. Eclipse Ganymed is a special C/C++ Development environment and accesible for every OS. Furthermore it is modular and you can also advance it to a MATLAB-like enviroment including the PyDev module and using python modules like numpy and scipy. It is also capable of accesing CVS trees directly. In my opinion this program package is flexible and helpful. Once everything is installed and configured it can be handled very easily. The other mentioned packages are Red-Hat, KDE, and GNOME development environments. However as I mentioned at the end it is a question of flavor. Best Regards, Flo Thanks. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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 -- Florian Dommert
Re: [gmx-users] Software for ESP fitting
2008/9/8 David van der Spoel [EMAIL PROTECTED] Vasilii Artyukhov wrote: Hi gmx-users, Sorry for a not-strictly-GROMACS-related question, but could someone suggest a program I could use to fit atomic charges to quantum chemistry results? antechamber. Thanks for a quick response, but does it accept anything except Gaussian output files as input for RESP? I wonder if I could use cube files for the procedure... Thanks in advance, Vasilii ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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 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] force field for boron-nitride nanotube
jj beh wrote: Dear all user How can I have a force field for simulation of boron-nitride nanotube? Has anything like that ever been simulated? If it hasn't, there may not be paramteers for such a species. I don't believe boron exists as an atom type in any of the force fields provided by Gromacs. If all of the above is true, you will have the (very hard) task of deriving new parameters for your nanotube. -Justin The pdb file of nanotube is as follow: HETATM1 N1 UNK 1 1.597 0.000 -5.015 1.00 0.00 N HETATM2 N2 UNK 1 1.129 1.129 -2.870 1.00 0.00 N HETATM3 B3 UNK 1 1.129 1.129 -4.291 1.00 0.00 B HETATM4 N4 UNK 1 0.000 1.597 -5.015 1.00 0.00 N HETATM5 N5 UNK 1 -1.129 1.129 -2.870 1.00 0.00 N HETATM6 B6 UNK 1 -1.129 1.129 -4.291 1.00 0.00 B HETATM7 N7 UNK 1 -1.597 0.000 -5.015 1.00 0.00 N HETATM8 N8 UNK 1 -1.129 -1.129 -2.870 1.00 0.00 N HETATM9 B9 UNK 1 -1.129 -1.129 -4.291 1.00 0.00 B HETATM 10 N10 UNK 1 0.000 -1.597 -5.015 1.00 0.00 N HETATM 11 N11 UNK 1 1.129 -1.129 -2.870 1.00 0.00 N HETATM 12 B12 UNK 1 1.129 -1.129 -4.291 1.00 0.00 B HETATM 13 N13 UNK 1 1.597 0.000 -0.724 1.00 0.00 N HETATM 14 B14 UNK 1 1.597 0.000 -2.145 1.00 0.00 B HETATM 15 N15 UNK 1 1.129 1.129 1.421 1.00 0.00 N HETATM 16 B16 UNK 1 1.129 1.129 0.000 1.00 0.00 B HETATM 17 N17 UNK 1 0.000 1.597 -0.724 1.00 0.00 N HETATM 18 B18 UNK 1 0.000 1.597 -2.145 1.00 0.00 B HETATM 19 N19 UNK 1 -1.129 1.129 1.421 1.00 0.00 N HETATM 20 B20 UNK 1 -1.129 1.129 0.000 1.00 0.00 B HETATM 21 N21 UNK 1 -1.597 0.000 -0.724 1.00 0.00 N HETATM 22 B22 UNK 1 -1.597 0.000 -2.145 1.00 0.00 B HETATM 23 N23 UNK 1 -1.129 -1.129 1.421 1.00 0.00 N HETATM 24 B24 UNK 1 -1.129 -1.129 0.000 1.00 0.00 B HETATM 25 N25 UNK 1 0.000 -1.597 -0.724 1.00 0.00 N HETATM 26 B26 UNK 1 0.000 -1.597 -2.145 1.00 0.00 B HETATM 27 N27 UNK 1 1.129 -1.129 1.421 1.00 0.00 N HETATM 28 B28 UNK 1 1.129 -1.129 0.000 1.00 0.00 B HETATM 29 N29 UNK 1 1.597 0.000 3.566 1.00 0.00 N HETATM 30 B30 UNK 1 1.597 0.000 2.145 1.00 0.00 B HETATM 31 B31 UNK 1 1.129 1.129 4.291 1.00 0.00 B HETATM 32 N32 UNK 1 0.000 1.597 3.566 1.00 0.00 N HETATM 33 B33 UNK 1 0.000 1.597 2.145 1.00 0.00 B HETATM 34 B34 UNK 1 -1.129 1.129 4.291 1.00 0.00 B HETATM 35 N35 UNK 1 -1.597 0.000 3.566 1.00 0.00 N HETATM 36 B36 UNK 1 -1.597 0.000 2.145 1.00 0.00 B HETATM 37 B37 UNK 1 -1.129 -1.129 4.291 1.00 0.00 B HETATM 38 N38 UNK 1 0.000 -1.597 3.566 1.00 0.00 N HETATM 39 B39 UNK 1 0.000 -1.597 2.145 1.00 0.00 B HETATM 40 B40 UNK 1 1.129 -1.129 4.291 1.00 0.00 B HETATM 41 H41 UNK 1 -2.140 0.000 -5.855 1.00 0.00 H HETATM 42 H42 UNK 1 0.000 2.140 -5.855 1.00 0.00 H HETATM 43 H43 UNK 1 2.140 0.000 -5.855 1.00 0.00 H HETATM 44 H44 UNK 1 0.000 -2.140 -5.855 1.00 0.00 H HETATM 45 H45 UNK 1 1.582 1.582 5.282 1.00 0.00 H HETATM 46 H46 UNK 1 1.582 -1.582 5.282 1.00 0.00 H HETATM 47 H47 UNK 1 -1.582 1.582 5.282 1.00 0.00 H HETATM 48 H48 UNK 1 -1.582 -1.582 5.282 1.00 0.00 H regards Javad ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg,
[gmx-users] Re[2]: trr file format
gurgo Vitaly Chaban wrote: Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Thanks. gurgo Make your life easier by just using the supplied functions to read the gurgo files. Check any analysis program. VC Thank you very much. Initially I supposed to write my trajectory VC analysis programme not in C (and thereby wanted to read trajectory VC from my programme) but after your suggestion and looking into VC the deeply hidden functions in gromacs I comply to code it in C using the VC already existing tools.:) However it seems to be very well if in the next version of the tutorial the exact format of trajectory files is explicitly shown. It will make life easier for many those who would like to compose their utilities not in C but for example in some scripting languages, etc. ___ 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] force field for boron-nitride nanotube
Dear all user How can I have a force field for simulation of boron-nitride nanotube? The pdb file of nanotube is as follow: HETATM1 N1 UNK 1 1.597 0.000 -5.015 1.00 0.00 N HETATM2 N2 UNK 1 1.129 1.129 -2.870 1.00 0.00 N HETATM3 B3 UNK 1 1.129 1.129 -4.291 1.00 0.00 B HETATM4 N4 UNK 1 0.000 1.597 -5.015 1.00 0.00 N HETATM5 N5 UNK 1 -1.129 1.129 -2.870 1.00 0.00 N HETATM6 B6 UNK 1 -1.129 1.129 -4.291 1.00 0.00 B HETATM7 N7 UNK 1 -1.597 0.000 -5.015 1.00 0.00 N HETATM8 N8 UNK 1 -1.129 -1.129 -2.870 1.00 0.00 N HETATM9 B9 UNK 1 -1.129 -1.129 -4.291 1.00 0.00 B HETATM 10 N10 UNK 1 0.000 -1.597 -5.015 1.00 0.00 N HETATM 11 N11 UNK 1 1.129 -1.129 -2.870 1.00 0.00 N HETATM 12 B12 UNK 1 1.129 -1.129 -4.291 1.00 0.00 B HETATM 13 N13 UNK 1 1.597 0.000 -0.724 1.00 0.00 N HETATM 14 B14 UNK 1 1.597 0.000 -2.145 1.00 0.00 B HETATM 15 N15 UNK 1 1.129 1.129 1.421 1.00 0.00 N HETATM 16 B16 UNK 1 1.129 1.129 0.000 1.00 0.00 B HETATM 17 N17 UNK 1 0.000 1.597 -0.724 1.00 0.00 N HETATM 18 B18 UNK 1 0.000 1.597 -2.145 1.00 0.00 B HETATM 19 N19 UNK 1 -1.129 1.129 1.421 1.00 0.00 N HETATM 20 B20 UNK 1 -1.129 1.129 0.000 1.00 0.00 B HETATM 21 N21 UNK 1 -1.597 0.000 -0.724 1.00 0.00 N HETATM 22 B22 UNK 1 -1.597 0.000 -2.145 1.00 0.00 B HETATM 23 N23 UNK 1 -1.129 -1.129 1.421 1.00 0.00 N HETATM 24 B24 UNK 1 -1.129 -1.129 0.000 1.00 0.00 B HETATM 25 N25 UNK 1 0.000 -1.597 -0.724 1.00 0.00 N HETATM 26 B26 UNK 1 0.000 -1.597 -2.145 1.00 0.00 B HETATM 27 N27 UNK 1 1.129 -1.129 1.421 1.00 0.00 N HETATM 28 B28 UNK 1 1.129 -1.129 0.000 1.00 0.00 B HETATM 29 N29 UNK 1 1.597 0.000 3.566 1.00 0.00 N HETATM 30 B30 UNK 1 1.597 0.000 2.145 1.00 0.00 B HETATM 31 B31 UNK 1 1.129 1.129 4.291 1.00 0.00 B HETATM 32 N32 UNK 1 0.000 1.597 3.566 1.00 0.00 N HETATM 33 B33 UNK 1 0.000 1.597 2.145 1.00 0.00 B HETATM 34 B34 UNK 1 -1.129 1.129 4.291 1.00 0.00 B HETATM 35 N35 UNK 1 -1.597 0.000 3.566 1.00 0.00 N HETATM 36 B36 UNK 1 -1.597 0.000 2.145 1.00 0.00 B HETATM 37 B37 UNK 1 -1.129 -1.129 4.291 1.00 0.00 B HETATM 38 N38 UNK 1 0.000 -1.597 3.566 1.00 0.00 N HETATM 39 B39 UNK 1 0.000 -1.597 2.145 1.00 0.00 B HETATM 40 B40 UNK 1 1.129 -1.129 4.291 1.00 0.00 B HETATM 41 H41 UNK 1 -2.140 0.000 -5.855 1.00 0.00 H HETATM 42 H42 UNK 1 0.000 2.140 -5.855 1.00 0.00 H HETATM 43 H43 UNK 1 2.140 0.000 -5.855 1.00 0.00 H HETATM 44 H44 UNK 1 0.000 -2.140 -5.855 1.00 0.00 H HETATM 45 H45 UNK 1 1.582 1.582 5.282 1.00 0.00 H HETATM 46 H46 UNK 1 1.582 -1.582 5.282 1.00 0.00 H HETATM 47 H47 UNK 1 -1.582 1.582 5.282 1.00 0.00 H HETATM 48 H48 UNK 1 -1.582 -1.582 5.282 1.00 0.00 H regards Javad ___ 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: force field for boron-nitride nanotube
Of course, there exist a bunch of works simulating B-N NTs. See papers. PDB file isn't enough to make a topology for gromacs. gurgo Has anything like that ever been simulated? If it hasn't, there may not be gurgo paramteers for such a species. I don't believe boron exists as an atom type in gurgo any of the force fields provided by Gromacs. gurgo If all of the above is true, you will have the (very hard) task of deriving new gurgo parameters for your nanotube. gurgo -Justin The pdb file of nanotube is as follow: HETATM1 N1 UNK 1 1.597 0.000 -5.015 1.00 0.00 N HETATM2 N2 UNK 1 1.129 1.129 -2.870 1.00 0.00 N HETATM3 B3 UNK 1 1.129 1.129 -4.291 1.00 0.00 B HETATM4 N4 UNK 1 0.000 1.597 -5.015 1.00 0.00 N HETATM5 N5 UNK 1 -1.129 1.129 -2.870 1.00 0.00 N HETATM6 B6 UNK 1 -1.129 1.129 -4.291 1.00 0.00 B HETATM7 N7 UNK 1 -1.597 0.000 -5.015 1.00 0.00 N HETATM8 N8 UNK 1 -1.129 -1.129 -2.870 1.00 0.00 N HETATM9 B9 UNK 1 -1.129 -1.129 -4.291 1.00 0.00 B HETATM 10 N10 UNK 1 0.000 -1.597 -5.015 1.00 0.00 N HETATM 11 N11 UNK 1 1.129 -1.129 -2.870 1.00 0.00 N HETATM 12 B12 UNK 1 1.129 -1.129 -4.291 1.00 0.00 B HETATM 13 N13 UNK 1 1.597 0.000 -0.724 1.00 0.00 N HETATM 14 B14 UNK 1 1.597 0.000 -2.145 1.00 0.00 B HETATM 15 N15 UNK 1 1.129 1.129 1.421 1.00 0.00 N HETATM 16 B16 UNK 1 1.129 1.129 0.000 1.00 0.00 B HETATM 17 N17 UNK 1 0.000 1.597 -0.724 1.00 0.00 N HETATM 18 B18 UNK 1 0.000 1.597 -2.145 1.00 0.00 B HETATM 19 N19 UNK 1 -1.129 1.129 1.421 1.00 0.00 N HETATM 20 B20 UNK 1 -1.129 1.129 0.000 1.00 0.00 B HETATM 21 N21 UNK 1 -1.597 0.000 -0.724 1.00 0.00 N HETATM 22 B22 UNK 1 -1.597 0.000 -2.145 1.00 0.00 B HETATM 23 N23 UNK 1 -1.129 -1.129 1.421 1.00 0.00 N HETATM 24 B24 UNK 1 -1.129 -1.129 0.000 1.00 0.00 B HETATM 25 N25 UNK 1 0.000 -1.597 -0.724 1.00 0.00 N HETATM 26 B26 UNK 1 0.000 -1.597 -2.145 1.00 0.00 B HETATM 27 N27 UNK 1 1.129 -1.129 1.421 1.00 0.00 N HETATM 28 B28 UNK 1 1.129 -1.129 0.000 1.00 0.00 B HETATM 29 N29 UNK 1 1.597 0.000 3.566 1.00 0.00 N HETATM 30 B30 UNK 1 1.597 0.000 2.145 1.00 0.00 B HETATM 31 B31 UNK 1 1.129 1.129 4.291 1.00 0.00 B HETATM 32 N32 UNK 1 0.000 1.597 3.566 1.00 0.00 N HETATM 33 B33 UNK 1 0.000 1.597 2.145 1.00 0.00 B HETATM 34 B34 UNK 1 -1.129 1.129 4.291 1.00 0.00 B HETATM 35 N35 UNK 1 -1.597 0.000 3.566 1.00 0.00 N HETATM 36 B36 UNK 1 -1.597 0.000 2.145 1.00 0.00 B HETATM 37 B37 UNK 1 -1.129 -1.129 4.291 1.00 0.00 B HETATM 38 N38 UNK 1 0.000 -1.597 3.566 1.00 0.00 N HETATM 39 B39 UNK 1 0.000 -1.597 2.145 1.00 0.00 B HETATM 40 B40 UNK 1 1.129 -1.129 4.291 1.00 0.00 B HETATM 41 H41 UNK 1 -2.140 0.000 -5.855 1.00 0.00 H HETATM 42 H42 UNK 1 0.000 2.140 -5.855 1.00 0.00 H HETATM 43 H43 UNK 1 2.140 0.000 -5.855 1.00 0.00 H HETATM 44 H44 UNK 1 0.000 -2.140 -5.855 1.00 0.00 H HETATM 45 H45 UNK 1 1.582 1.582 5.282 1.00 0.00 H HETATM 46 H46 UNK 1 1.582 -1.582 5.282 1.00 0.00 H HETATM 47 H47 UNK 1 -1.582 1.582 5.282 1.00 0.00 H HETATM 48 H48 UNK 1 -1.582 -1.582 5.282 1.00 0.00 H regards Javad -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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
[gmx-users] sn1 and sn2 chains of popc
Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2? Thanks for your help.___ 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] manipulation of trajectory data
Hello GROMACS users! I would like to preform arithmetic operations on trajectories which are output from GROMACS simulations (e.g., to multiply the velocity of atom 1 by that of atom 2, and average over time). I have read in the mailing lists references to g_traj and other functions, but think the more straightforward approach is to write a C code that can access the GROMACS trajectory data and perform what I ask it to. This is said to be done using the template C code in template.c. Can anyone send me a SIMPLE example of such a C program? The file template.c has many comments, but I find it hard to understand. If anyone has a simpler example along the lines of my interests, please send me it! Thanks very much in advance, -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. ___ 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] Fatel error in simulated annealing
ravi sharma wrote: hi you have written that in my file there are some trailing characters, how can identify these characters ?? You can see them in the vi editor. -Justin ;simulated annealing annealing = single^M annealing_npoints = 5 ^M annealing_time = 2 500 1000 1500 2000^M annealing_temp = 300 350 400 450 450^M --- On *Mon, 8/9/08, Justin A. Lemkul /[EMAIL PROTECTED]/* wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Fatel error in simulated annealing To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, 8 September, 2008, 3:28 PM ravi sharma wrote: Thanks justin, but how can identify these groups, i am using fedora core 8, also Thanks for the Tc-grps, What groups are you talking about, tc-grps? Please be more specific. -Justin regards, --- On *Sun, 7/9/08, Justin A. Lemkul /[EMAIL PROTECTED]/* wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Fatel error in simulated annealing To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sunday, 7 September, 2008, 10:28 PM You have trailing characters in your simulated annealing section: What shows up for me is: ;simulated annealing annealing = single^M annealing_npoints = 5 ^M annealing_time = 2 500 1000 1500 2000^M annealing_temp = 300 350 400 450 450^M Are you transferring between Windows and Linux/Mac/etc. systems? If so, you will need to process your .mdp file with dos2unix. Unsolicited advice on T-coupling: tc-grps = Protein SOL HEM NA+ It's a bad idea to couple solvent, ions, and small molecules all in different tc-grps. Reference here for information regarding thermostats: http://wiki.gromacs.org/index.php/thermostats -Justin ravi sharma wrote: Hello guys, i am doing a simulation with simulated annealing of a protein which contains heme inside, the normal without simulated annealing its running fine but while m writing simulated annealing in my md.mdp its showing error //Fatal error: Not enough annealing values: 1 (for 4 groups) http://www.gromacs.org/mailman/listinfo/gmx-users// I am attaching my md.mdp file here md.mdp Thanks Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On *Sun, 7/9/08, Florian Dommert /[EMAIL PROTECTED]/* wrote: From: Florian Dommert [EMAIL PROTECTED] Subject: Re: [gmx-users] trr file format To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sunday, 7 September, 2008, 4:54 PM On 06.09.2008, at 22:28, Vitaly Chaban wrote: Hello, Where can I read about the exact format of the TRR and XTC files. I mean the width and type of every field in the binary trajectory file. I see read_'next_frame(status,fr)' function in 'template.c'. But where is this fuction defined? Sorry, I'm not an expert in C. :( Hello, if you have problems, finding appropiate header files for the functions of gmx, you can perhaps use a development environment like Eclipse, Source-Navigator, KDevelop, Anjuta depending on your flavour and operating system. This programs index all the functions in a specified project and you can look up their definitions by request without searching the files of the complete src-code. It is hard to rank the different programs due to their various capabilities and your requirements. Eclipse Ganymed is a special C/C++ Development environment and accesible for every OS. Furthermore it is modular and you can also advance it to a MATLAB-like
[gmx-users] Software for ESP fitting
Hi gmx-users, Sorry for a not-strictly-GROMACS-related question, but could someone suggest a program I could use to fit atomic charges to quantum chemistry results? Thanks in advance, Vasilii ___ 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] CPMD- QM MM simulation
Hi. Anyway, it would be nice to have a structured manual for the GMX/CPMD interface. The website http://www.tougaloo.edu/research/qmmm has just a few basic information and further information in this mailing list under http://www.gromacs.org/pipermail/gmx-users/2006-June/022329.html are not that easy to understand. A small guide on how to input new ions into the source code for users how normally do not deal with source code so much for ex. would be nice in such a manual. Or a picture of the MMlayer_radii and qmmmcoul_cutoff with some explanations... It takes a long time to find these things out by try and error and reading the source code. Christian. On Mon, 2008-09-08 at 09:29 +0200, Gerrit Groenhof wrote: Message: 1 Date: Fri, 5 Sep 2008 15:48:12 -0700 From: Chih-Ying Lin [EMAIL PROTECTED] Subject: [gmx-users] CPMD- QM MM simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi I read some papers, which the authors use CPMD - QM MM simulation to reparametrize the force field parameters. But, they did not say the details. Could anyone explain this more here? Why don't you contact the authors? Gerrit -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ 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] sn1 and sn2 chains of popc
Thanks Justin for your reply you mean to say that C32 of glycerol involves in the palimotyl chain formation so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl chain formation so call as sn2. Am I correct? Thanks in advance. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2? It derives from the numbering of the carbons on the glycerol backbone. -Justin Thanks for your help. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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] sn1 and sn2 chains of popc
minnale wrote: Thanks Justin for your reply you mean to say that C32 of glycerol involves in the palimotyl chain formation so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl chain formation so call as sn2. Am I correct? More or less, let's just get a few things straight. Numbering like C32, C12, C13, etc. is a scheme devised to give sensible atomic numbering to all atoms in a 50 (or more)-atom lipid, but is not the same numbering scheme applied in conventional lipid numbering from Biochemistry lessons. To me, C32 has absolutely no bearing on sn-1. Look at the structure of glycerol: CH2OH | HO--C--H | CH2OH The second carbon is a chiral center, and (as I was taught in Biochemistry), that is where we derive the sn nomenclature: sn-2 = stereospecific number 2. The other carbons are given the obvious numbers of 1 and 3. By convention, the phosphate headgroup is assigned to carbon 3. Therefore, chain 1 is on the sn-1 carbon, and chain 2 is on sn-2. -Justin Thanks in advance. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2? It derives from the numbering of the carbons on the glycerol backbone. -Justin Thanks for your help. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant 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://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: trr file format
Thank you! After a day of searches I found the function body I wanted. :) gurgo Hello, gurgo if you have problems, finding appropiate header files for the gurgo functions of gmx, you can perhaps use a development environment like gurgo Eclipse, Source-Navigator, KDevelop, Anjuta depending on your flavour gurgo and operating system. gurgo This programs index all the functions in a specified project and you gurgo can look up their definitions by request without searching the files gurgo of the complete src-code. gurgo It is hard to rank the different programs due to their various gurgo capabilities and your requirements. gurgo Eclipse Ganymed is a special C/C++ Development environment and gurgo accesible for every OS. Furthermore it is modular and you can also gurgo advance it to a MATLAB-like enviroment including the PyDev module and gurgo using python modules like numpy and scipy. It is also capable of gurgo accesing CVS trees directly. In my opinion this program package is gurgo flexible and helpful. Once everything is installed and configured it gurgo can be handled very easily. gurgo The other mentioned packages are Red-Hat, KDE, and GNOME development gurgo environments. However as I mentioned at the end it is a question of gurgo flavor. gurgo Best Regards, gurgo Flo -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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: manipulation of trajectory data
gurgo If anyone has a simpler example along the lines of my interests, gurgo please send me it! and to me... ___ 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] RE: manipulation of trajectory data
to me too. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 16:30, Vitaly Chaban [EMAIL PROTECTED]wrote: gurgo If anyone has a simpler example along the lines of my interests, gurgo please send me it! and to me... ___ 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 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[2]: manipulation of trajectory data
OM to me too. OM OM Koby Levy research group, OM Weizmann Institute of Science. OM http://www.weizmann.ac.il/sb/faculty_pages/Levy/ It sounds like an epidemic of analyzing gromacs trajectories. :) -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email:[EMAIL PROTECTED] skype: vvchaban ___ 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] installation problem: undefined symbols: _gmx_fft_(init_)3d_real
Dear all, I would like to ask you help on an installation issue of GROMACS. When I am running ''make'' after configuring GROMACS, I get the following error: /usr/libexec/gcc/i686-apple-darwin8/4.2.1/ld: undefined symbols: _gmx_fft_3d_real _gmx_fft_init_3d_real Collect2: ld returned 1 exit status Make[3]: *** [mdrun] Error 1 Make[2]: *** [all-recursive] Error 1 Make[1]: *** [all] Error 2 Make: *** [all-recursive] Error 1 This clearly relates to the FFTW program I have already successfully installed, but I don't see why this happens. Has anyone else confronted this problem and solved it? I would appreciate any help! As additional info, I use Intel Mac Core Duo machine and I have gcc 4.2 installed with the XCode tools 2.5. Greetings, Henri Ervasti -- Dr. Henri K. Ervasti Dutch Separation Technology Institute (DSTI) Stationsstraat 77, 3811 MH Amersfoort The Netherlands tel. +31 33 467 6241 mob. +31 6 2625 4987 e-mail [EMAIL PROTECTED] ___ 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: Re[6]: Using Morse potentials with ENCAD force field
I am trying to make a radial temperature profile of a given thickness. I originally used the confout.gro file containing the final output of velocity and position of each atom to calculate the temperature from the velocity but would like to take time averages now. Andy On Sat, Sep 6, 2008 at 4:21 AM, Vitaly Chaban [EMAIL PROTECTED]wrote: AS The system works now, thanks for finding a simple mistake. Another question I had is if I want to calculate the average velocities of all the atoms over a period of time can I use g_traj to create an average velocity of the atoms, but looking at all_veloc.xvg file the atom number starts at 0 so I don't know where to cross reference it with another file to coordinates of that atom. Is there a function in GROMACS that will give averages of velocities and positions of atoms? AS I think you can find the average atom velocity from of temperature of the system. Telling the truth I don't know why you want ones. If you tell the final result you need probably I can be of more use. I don't really remember from what number the atoms numbering starts in the programme you speak about but if it starts from zero this corresponds to the first atom in your conf.gro. AS Thanks, AS Andy -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ 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] Fatel error in simulated annealing
ravi sharma wrote: Hello justin, whether i do correct my md.mdp by vi editor but still it was giving error well i removed all those groups which coupling to thermostat now its working (NA+ HEME SOL) I guess I hadn't even considered that. If you're doing simulated annealing, and progressively changing the temperature, you probably shouldn't be trying to constrain the elements of your system to a single temperature! -Justin (Please remember to keep discussions on the gmx-users list, for example, using Reply All so that the discussion may be archived for the benefit of future users) Thanks, Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On *Mon, 8/9/08, Justin A. Lemkul /[EMAIL PROTECTED]/* wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Fatel error in simulated annealing To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, 8 September, 2008, 5:00 PM ravi sharma wrote: hi you have written that in my file there are some trailing characters, how can identify these characters ?? You can see them in the vi editor. -Justin ;simulated annealing annealing = single^M annealing_npoints = 5 ^M annealing_time = 2 500 1000 1500 2000^M annealing_temp = 300 350 400 450 450^M --- On *Mon, 8/9/08, Justin A. Lemkul /[EMAIL PROTECTED]/* wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Fatel error in simulated annealing To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, 8 September, 2008, 3:28 PM ravi sharma wrote: Thanks justin, but how can identify these groups, i am using fedora core 8, also Thanks for the Tc-grps, What groups are you talking about, tc-grps? Please be more specific. -Justin regards, --- On *Sun, 7/9/08, Justin A. Lemkul /[EMAIL PROTECTED]/* wrote: From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Fatel error in simulated annealing To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Sunday, 7 September, 2008, 10:28 PM You have trailing characters in your simulated annealing section: What shows up for me is: ;simulated annealing annealing = single^M annealing_npoints = 5 ^M annealing_time = 2 500 1000 1500 2000^M annealing_temp = 300 350 400 450 450^M Are you transferring between Windows and Linux/Mac/etc. systems? If so, you will need to process your .mdp file with dos2unix. Unsolicited advice on T-coupling: tc-grps = Protein SOL HEM NA+ It's a bad idea to couple solvent, ions, and small molecules all in different tc-grps. Reference here for information regarding thermostats: http://wiki.gromacs.org/index.php/thermostats -Justin ravi sharma wrote: Hello guys, i am doing a simulation with simulated annealing of a protein which contains heme inside, the normal without simulated annealing its running fine but while m writing simulated annealing in my md.mdp its showing error //Fatal error: Not enough annealing values: 1 (for 4 groups) http://www.gromacs.org/mailman/listinfo/gmx-users// I am attaching my md.mdp file here md.mdp Thanks Ravi Datta Sharma Lecturer, Bioinformatics, Department of Microbiology, CCS Unversity, Meerut --- On *Sun, 7/9/08, Florian Dommert /[EMAIL PROTECTED]/* wrote: From: Florian Dommert [EMAIL
[gmx-users] optimizing the mailing list
I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow submitters to flag messages as belonging to some particular topic(s). e.g. program crash force fields protein free energy coarse graining lipids and detergents unknown etc. Since the submission is by regular email and hence there is no possibility of introducing a radio box with topic options, this could be implemented by allowing any user to define the topic to which a particular message belongs. Ideally, the submitter would go to the website after submission and set the topic of their own submission. If the archives then allowed a user to view only a particular topic, then this would offer an alternative to the search tool, and also a link to such a topical list could be posted in the relevant pages on the wiki. I realize that the actual coding of such an interface may not be available at this time. But I suspect that somebody on this list knows some type of useful optimizations that are possible at this time. Chris. ___ 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] How to convert gromacs traj file(.xtc) to amber traj file?
Hi, Everyone, I just want to use the clustering tool in amber which only take trj file. Thanks -Ranqi _ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008___ 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: optimizing the mailing list
it's called internet forum... :) I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow submitters to flag messages as belonging to some particular topic(s). e.g. program crash force fields protein free energy coarse graining lipids and detergents unknown etc. Since the submission is by regular email and hence there is no possibility of introducing a radio box with topic options, this could be implemented by allowing any user to define the topic to which a particular message belongs. Ideally, the submitter would go to the website after submission and set the topic of their own submission. If the archives then allowed a user to view only a particular topic, then this would offer an alternative to the search tool, and also a link to such a topical list could be posted in the relevant pages on the wiki. I realize that the actual coding of such an interface may not be available at this time. But I suspect that somebody on this list knows some type of useful optimizations that are possible at this time. Chris. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ 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] still some problems with HP-UX... grompp acting weird
Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: 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 (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/ gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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
