[gmx-users] Re: topolbuild1_2_1.tgz decompressing problem
Hello, I downloaded topolbuild1_2_1.tgz from the URL: http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz It seems you are right. I tried the same and also found the archive broken. Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, cell.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] reg mopac gromacs installation
vidhya sankar wrote: dear gmx user , i am doing QM/MM using MOPAC/GROMACS when i configure mopac7-1.10 the software using for the interface with gromacs by ../configure command i got error as follows configure error: f2c or g2c library cannot be found . solution for the above error would be appericiated reply please thanks in advance Solution: install f2c or g2c. Google is your friend. Probably the installation documentation for this port of GROMACS should talk about this issue. 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
Re: [gmx-users] very strange domain composition statistics
Jennifer Williams wrote: Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hi, Thanks for your input. Sorry I should have mentioned that I am using the latest version of gromacs (4.0.5). This morning I noticed that the strange domain decomp statistics are only produced when my simulations run on certain nodes. Below I have pasted the domain decomp statistics for the SAME .tpr file run on 2 different nodes (each time using 6 nodes)- the first looks ok to me while the second produces crazy numbers. Indeed, one looks quite normal. I have opened a call to computer support at my Uni to ask if there is some difference between the nodes and for now I specify that my simulations should run on certain nodes which I have checked are ok. I don't know if this is something to do with the way I compiled gromacs or the architecture. I did a standard installation and it seemed to run smoothly-no error messages. I have attached my config.log. Seems like some nodes might have a suitable source of timing routines, and some might not. It ought to have nothing to do with how GROMACS was compiled if the cluster is homogeneous. If the cluster's nodes are not homogeneous then the admins should know about it, and have documented how to deal with some issues. Mark If you have any ideas please let me know, Thanks D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 1967.2 av. #atoms communicated per step for LINCS: 2 x 20.4 Average load imbalance: 30.3 % Part of the total run time spent waiting due to load imbalance: 5.8 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % NOTE: 5.8 % performance was lost due to load imbalance in the domain decomposition. R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 6 11 852.216 341.9 3.0 Comm. coord. 6101 594.411 238.5 2.1 Neighbor search6 11 2271.294 911.2 7.9 Force 6101 5560.129 2230.519.3 Wait + Comm. F 6101 1216.171 487.9 4.2 PME mesh 610115071.432 6046.152.2 Write traj.6 10012.5771.0 0.0 Update 6101 264.545 106.1 0.9 Constraints6101 923.418 370.4 3.2 Comm. energies 6101 942.036 377.9 3.3 Rest 61167.866 468.5 4.0 --- Total 6 28866.09611580.0 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1930.000 1930.000100.0 32:10 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 51.737 6.922 44.767 0.536 Finished mdrun on node 0 Fri Jul 31 13:05:01 2009 D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 1969.0 av. #atoms communicated per step for LINCS: 2 x 15.7 Average load imbalance: 500.0 % Part of the total run time spent waiting due to load imbalance: 5822746112.0 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % NOTE: 5822746112.0 % performance was lost due to load imbalance in the domain decomposition. R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Write traj.6 1001 18443320128.89043061.8 100.0 Update 6101 314.1750.0 0.0 Rest 69223372036.85521534.950.0 --- Total 618443397799.33643062.0 100.0 --- NOTE: 306 % of the run time was spent communicating energies, you might want to use the -nosum option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 7177.000 7177.000100.0 1h59:37 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 13.907 1.861 12.038 1.994 Finished mdrun on node 0 Thu Jul 30 01:47:05 2009 Quoting Berk Hess g...@hotmail.com: Date: Fri, 31 Jul 2009 07:49:49 +0200 From: sp...@xray.bmc.uu.se To:
[gmx-users] g_wham problem
Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is accomp...@student.dlut.edu.cn Thanks a lot Jiaqi ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ 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] g_wham problem
accomp lin wrote: Dear all Gromacs 3.3.3 seems to have a problem with g_wham and there is a fixed version from David Bostick of Scripps. So, does anybody has this fixed version of g_wham or is there anybody know that where I can find it? My email address is accomp...@student.dlut.edu.cn mailto:accomp...@student.dlut.edu.cn The Gromacs 4.0.x series contains a fixed g_wham that can handle the .pdo output of Gromacs 3.3.x. Using this official version might make it easier to get technical support, should you need it. -Justin Thanks a lot Jiaqi 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] desciption of ffG43a1bon.itp
Hello In the file ffG43a1bon.itp, the bond parameters are given like this- -- ICB(H)[N] CB[N] B0[N] ; #define gb_1 0. 1000 1.5700e+07 ; H - OA 750 ; #define gb_2 0. 1000 1.8700e+07 ; H - N (all) 895 ; #define gb_3 0. 1090 1.2300e+07 ; HC - C 700 Can anybody please tell me, which one is is the force constant and which one is ideal bond length. For describing a new bond parameters , what the values I have to provide in the file ffG43a1bon.itp. The ffG43a1bon.itp is not clearly described in the chapter5 of the manual of gromacs version4. Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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
