Re: [gmx-users] error message during make after gtomacs configuration
On 10/03/2012 5:52 PM, Dialing Pretty wrote: Dear All, My command is ./configure --disable-threads Thanks. You do need --disable-threads, as noted by the Cygwin installation guide. Your earlier errors looked consistent with not having used it. The error message are as following. I am looking forward to getting a message from you on how to avoid the error message. I do observe intermittent issues with builds on Cygwin that look somewhat similar to the ones you suggest. Re-running make eventually succeeds. I expect this is some upstream issue that has nothing to do with GROMACS. Mark Cheers, Dialing /bin/sh ../../../libtool --tag=CC--mode=compile cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2-I../../../include-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -fexcess-precision=fast -MT sdot.lo -MD -MP -MF .deps/sdot.Tpo -c -o sdot.lo sdot.c make[4]: execvp: /bin/sh: Bad address ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: retry: Resource temporarily unavailable ../../../libtool: fork: Resource temporarily unavailable Makefile:338: recipe for target `sdot.lo' failed make[4]: *** [sdot.lo] Error 254 make[4]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib/gmx_blas' Makefile:599: recipe for target `all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, 10 March 2012 2:07 PM *Subject:* Re: [gmx-users] error message during make after gtomacs configuration On 10/03/2012 2:50 PM, Dialing Pretty wrote: Dear All, After I run the Gromacs 4.5.5 configuration (in this step there is no error), I run make, but I meet the following error messages. Will you please give me some suggestions on how to avoid these error messages? No. You haven't told us your configure command, so we're not going to guess what you're doing wrong. Mark Cheers, Dialing numa_malloc.c:151:5: error: 'smalloc_GetCurrentProcessorNumberEx' undeclared (first use in this function) numa_malloc.c:151:5: note: each undeclared identifier is reported only once for each function it appears in numa_malloc.c:151:44: error: 'func_GetCurrentProcessorNumberEx_t' undeclared (first use in this function) numa_malloc.c:151:79: error: expected ';' before 'GetProcAddress' numa_malloc.c:152:5: error: 'smalloc_GetNumaProcessorNodeEx' undeclared (first use in this function) numa_malloc.c:152:39: error: 'func_GetNumaProcessorNodeEx_t' undeclared (first use in this function) numa_malloc.c:152:69: error: expected ';' before 'GetProcAddress' numa_malloc.c: In function 'ReturnHeapHandle': numa_malloc.c:246:5: error: 'PROCESSOR_NUMBER' undeclared (first use in this function) numa_malloc.c:246:22: error: expected ';' before 'CurrentProcessorNumber' numa_malloc.c:285:5: warning: implicit declaration of function 'smalloc_GetCurrentProcessorNumberEx' numa_malloc.c:285:42: error: 'CurrentProcessorNumber' undeclared (first use in this function) numa_malloc.c:287:5: warning: implicit declaration of function 'smalloc_GetNumaProcessorNodeEx' numa_malloc.c:324:9: warning: implicit declaration of function 'HeapSetInformation' Makefile:332: recipe for target `numa_malloc.lo' failed make[4]: *** [numa_malloc.lo] Error 1 make[4]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib/thread_mpi' Makefile:599: recipe for target `all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post
[gmx-users] g_dist without output file
Dear all When I use g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5, program was done without error, but it don't create output file (dist.xvg) in the directory in which g_dist tool was run. What is reason of this case? Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_spatial (gromacs 4.5 manual)
Dear gromacs users I read g_spatial tool of gromacs 4.5 manual. I have many questions. There are in the manual: USAGE: 1. Use make ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run g spatial on the xtc output of step #3. 5. Load grid.cube into VMD and view as an isosurface. In the step 2, [-center tric -ur compact -pbc none] is true or [-center -ur compact -pbc none]? In determination of SDF, there are 2 groups: for example; SDF of the first (1) group around second (2) group. In the step 2 of above usage, we should select two groups of the index file, for centering and for output. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case (all of the system). In the step 3 of above usage, we should select two groups of the index file, for least squares fit and for output. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case (all of the system). In the step 4 of above usage, we should select two groups of the index file, to generate SDF and to output cords. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case. Please answer my question exactly with determining group numbers in the each step. Any help will highly appreciated. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear all When I use g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5, program was done without error, but it don't create output file (dist.xvg) in the directory in which g_dist tool was run. What is reason of this case? Try without the -dist 0.5, you will get the -o dist.xvg output. the -dist is Print all atoms in group 2 closer than dist to the center of mass of group 1 Any help will highly appreciated. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dist without output file
Dear Lina Thanks for your reply. Without the -dist 0.5, I get the -o dist.xvg output, but I need list of the all atoms in group 2 closer than dist to the center of mass of group 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina Thanks for your reply. Without the -dist 0.5, I get the -o dist.xvg output, but I need list of the all atoms in group 2 closer than dist to the center of mass of group 1. It print on the terminal, you may notice it. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: questions about Principal Component Analysis
Regarding my second question, I have been experimenting with the cosine content using different portions of the trajectory and these are the results I got for the first principal component: proj-ev1_coscont_0-5ns.xvg 0.0174761 proj-ev1_coscont_0-10ns.xvg 0.0283423 proj-ev1_coscont_0-15ns.xvg 4.16906e-06 proj-ev1_coscont_0-20ns.xvg 0.0689592 proj-ev1_coscont_0-25ns.xvg 0.161691 proj-ev1_coscont_0-30ns.xvg 0.298431 proj-ev1_coscont_0-35ns.xvg 0.535732 proj-ev1_coscont_0-40ns.xvg 0.767029 proj-ev1_coscont_0-45ns.xvg 0.885829 proj-ev1_coscont_0-50ns.xvg 0.906473 proj-ev1_coscont_5-50ns.xvg 0.8823 proj-ev1_coscont_10-50ns.xvg 0.751018 proj-ev1_coscont_15-50ns.xvg 0.537473 proj-ev1_coscont_20-50ns.xvg 0.357136 proj-ev1_coscont_25-50ns.xvg 0.145889 proj-ev1_coscont_30-50ns.xvg 0.0150995 proj-ev1_coscont_35-50ns.xvg 0.00123905 proj-ev1_coscont_40-50ns.xvg 0.00675679 proj-ev1_coscont_45-50ns.xvg 0.0105643 The total time I have run the simulation was 70ns, but judging from the steep increase of the RMSD (RMSD plot attached), I decided to exclude the first 20ns from the analysis. Hence the cosine content values above correspond to the last 50ns and the counting starts from the 20th ns. Clearly the convergence of the last 50ns is not good (proj-ev1_coscont_0-50ns.xvg: 0.906473), but the PC1 plot (attached) shows a steep decrease at ~30ns which looks like a conformational transition. It is also evident that the cosine content decreases drastically approximately at that point (25-50ns: 0.145889, 30-50ns.xvg: 0.0150995, 35-50ns.xvg: 0.00123905, etc.) and reached values that are not bad. Unfortunately, extending the simulation is not an option due to lack of time (I am forced to finish the manuscript soon). So would you recommend doing essential dynamics for the last 20ns? I would GREATLY appreciate any comments!!! Thomas On 7 March 2012 21:56, Thomas Evangelidis teva...@gmail.com wrote: Dear GROMACS community, I have two questions regarding PCA. I have run MD simulations for 70 ns for a protein of 1100 amino acids, of which I decided - based on the RMSD - to analyze the last 50. 1) The protein consists of 5 domains, out of which only one is of interest in this study. Is it right to do draw conclusion from PCA restricted that domain (400 aa)? 2) How can I find out if the simulation time is sufficient to do PCA? Thanks in advance for any feedback. Thomas attachment: proj-ev1.pngattachment: totalWT+C2_70ns_protein_caRMSDvsTIME.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dist without output file
Dear Lina There is not any things related to list of atoms on the terminal. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] genconf,grompp
Hi all In the following you can see the format of H-largebox.gro including my desired number of atoms, but when I apply the following grompp command with and with out maxwarn I see the following error: --- Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Rat-tat-tat Ka boom boom (The Smashing Pumpkins) genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1 Great Red Owns Many ACres of Sand 6 1DRGCAA1 0.495 -0.175 -0.072 0. 0. 0. 1DRGCAB2 0.483 -0.311 -0.143 0. 0. 0. 1DRGCAC3 0.388 -0.406 -0.069 0. 0. 0. 1DRGCAD4 0.451 -0.463 0.058 0. 0. 0. 1DRGCAE5 0.352 -0.557 0.127 0. 0. 0. 1DRGCAF6 0.415 -0.613 0.255 0. 0. 0. 2DRGCAA7 0.495 -0.175 -0.072 0. 0. 0. 2DRGCAB8 0.483 -0.311 -0.143 0. 0. 0. 2DRGCAC9 0.388 -0.406 -0.069 0. 0. 0. 2DRGCAD 10 0.451 -0.463 0.058 0. 0. 0. 2DRGCAE 11 0.352 -0.557 0.127 0. 0. 0. 2DRGCAF 12 0.415 -0.613 0.255 0. 0. 0. 3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0. 3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0. Thanks Nahid -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina There is not any things related to list of atoms on the terminal. t: 100 83 ILE 845 CG1 1.60274 (nm) t: 100 83 ILE 846 CG2 1.63838 (nm) t: 100 83 ILE 847 CD 1.59769 (nm) t: 100 83 ILE 848 C 1.8202 (nm) t: 100 83 ILE 849 O 1.86972 (nm) t: 100 84 ALA 850 N 1.88309 (nm) t: 100 84 ALA 851 H 1.85958 (nm) t: 100 84 ALA 853 CB 1.99705 (nm) Last frame 50 time 100.000 gcq#310: Shoot them the atom now (The Ramones) g_dist_g -f try_1.xtc -s try_1.tpr -dt 5 -b 0 -e 100 -dist 2 -n index_1.ndx Best regards -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Lina There is not any things related to list of atoms on the terminal. Might your distance -dist so large. try a smaller one and see. Best regards -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genconf,grompp
You haven't answered any of the questions I asked in my previous reply: http://lists.gromacs.org/pipermail/gmx-users/2012-March/069235.html If you want free help, you have to be willing to make it easy. We can't see inside your mind as to what's going on. None of the information you have posted is suggestive of any error, and we don't even know what the error message is because you haven't posted it (scroll up in your terminal). -Justin saly jackson wrote: Hi all In the following you can see the format of H-largebox.gro including my desired number of atoms, but when I apply the following grompp command with and with out maxwarn I see the following error: --- Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Rat-tat-tat Ka boom boom (The Smashing Pumpkins) genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1 Great Red Owns Many ACres of Sand 6 1DRGCAA1 0.495 -0.175 -0.072 0. 0. 0. 1DRGCAB2 0.483 -0.311 -0.143 0. 0. 0. 1DRGCAC3 0.388 -0.406 -0.069 0. 0. 0. 1DRGCAD4 0.451 -0.463 0.058 0. 0. 0. 1DRGCAE5 0.352 -0.557 0.127 0. 0. 0. 1DRGCAF6 0.415 -0.613 0.255 0. 0. 0. 2DRGCAA7 0.495 -0.175 -0.072 0. 0. 0. 2DRGCAB8 0.483 -0.311 -0.143 0. 0. 0. 2DRGCAC9 0.388 -0.406 -0.069 0. 0. 0. 2DRGCAD 10 0.451 -0.463 0.058 0. 0. 0. 2DRGCAE 11 0.352 -0.557 0.127 0. 0. 0. 2DRGCAF 12 0.415 -0.613 0.255 0. 0. 0. 3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0. 3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0. Thanks Nahid -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Resources on simulation walls
Hi, Only if you have time, do you know of any resources that explain the concept of a Gromacs wall, which seems related to 2-D Ewald summation? In the Gromacs 4.5.4 manual, the parameters related to walls are described on page 182, and also on http://manual.gromacs.org/current/online/mdp_opt.html#walls . But do you know of any general explanations, books, or literature papers that would help me to understand what a wall does and why and when I need to use them? I cannot seem to find them discussed in the main Gromacs papers ( http://www.gromacs.org/Documentation/Gromacs_papers ). Also, is there another name for a simulation wall? When I use Google to search for MD simulation wall, it is not clear that I am looking for the correct thing. Thanks so much for your time. Andrew DeYoung Carnegie Mellon 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Resources on simulation walls
Hi Andrew, at http://manual.gromacs.org/online/mdp_opt.html#nl the manual says: Without walls or with only one wall the system size is infinite in the z direction. Therefore pressure coupling or Ewald summation methods can not be used. These disadvantages do not apply when two walls are used So I guess wall are physical walls, i.e. something limitating the expansion of your system in the z-direction. In the xy plane the system is replicated because of pbc but, without walls, it would be unlimited in the z-direction. Il 10/03/2012 17:46, Andrew DeYoung ha scritto: Hi, Only if you have time, do you know of any resources that explain the concept of a Gromacs wall, which seems related to 2-D Ewald summation? In the Gromacs 4.5.4 manual, the parameters related to walls are described on page 182, and also on http://manual.gromacs.org/current/online/mdp_opt.html#walls . But do you know of any general explanations, books, or literature papers that would help me to understand what a wall does and why and when I need to use them? I cannot seem to find them discussed in the main Gromacs papers ( http://www.gromacs.org/Documentation/Gromacs_papers ). Also, is there another name for a simulation wall? When I use Google to search for MD simulation wall, it is not clear that I am looking for the correct thing. Thanks so much for your time. Andrew DeYoung Carnegie Mellon 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Charge delocalization fullerene
Dear all, I am trying to realistically de-localize a charge over all the carbon atoms of a fullerene. Up to now I just put 1/60 on each and a contra-ion far away from the bucky ball. I do not believe this is the best approach but i can not think on a better solution as I started with gromacs two months ago. It would be very nice if you can indicate which would be the best way of doing this. I heard about shell model but there is no many information available. Please let me now if you need any extra information. Thank you very much in advance for any comment regarding this problem. R -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Resources on simulation walls
Hi, Only if you have time, do you know of any resources that explain the concept of a Gromacs wall, which seems related to 2-D Ewald summation? In the Gromacs 4.5.4 manual, the parameters related to walls are described on page 182, and also on http://manual.gromacs.org/current/online/mdp_opt.html#walls . But do you know of any general explanations, books, or literature papers that would help me to understand what a wall does and why and when I need to use them? I cannot seem to find them discussed in the main Gromacs papers ( http://www.gromacs.org/Documentation/Gromacs_papers ). Also, is there another name for a simulation wall? When I use Google to search for MD simulation wall, it is not clear that I am looking for the correct thing. If I recollect correctly, the gromacs wall provides elastic collision for the particles approaching it. There was some discussion of this matter in this list around February-March, 2009, browse archives... -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs 4.5.5 cygwin installation error message
Dear All, For Gromacs installation, my configure command is: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads. After make, the error message is as following. I am looking forward to getting a reply from you on how to avoid the error message. Wholly . .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_fftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la' failed make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
Is fftw3 properly installed in /usr/local/lib? On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote: Dear All, For Gromacs installation, my configure command is: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads. After make, the error message is as following. I am looking forward to getting a reply from you on how to avoid the error message. Wholly . .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_fftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la' failed make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
On 11/03/2012 12:20 PM, Peter C. Lai wrote: Is fftw3 properly installed in /usr/local/lib? And of the right precision, like reading the installation guides will warn you... Mark On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote: Dear All, For Gromacs installation, my configure command is: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads. After make, the error message is as following. I am looking forward to getting a reply from you on how to avoid the error message. Wholly . .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_fftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la' failed make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
Hi Mark, If for Gromacs I use disable --disable-threads, for fftw3 show I also use --disable-threads? Wholley From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 11 March 2012 11:43 AM Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message On 11/03/2012 12:20 PM, Peter C. Lai wrote: Is fftw3 properly installed in /usr/local/lib? And of the right precision, like reading the installation guides will warn you... Mark On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote: Dear All, For Gromacs installation, my configure command is: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads. After make, the error message is as following. I am looking forward to getting a reply from you on how to avoid the error message. Wholly . .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_fftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la' failed make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
I don't think fftw3 has that option, since disable-threads pertains to mdrun parallelization (forces MPI-only, basically). On 2012-03-10 05:50:19PM -0800, Wholly Peach wrote: Hi Mark, If for Gromacs I use disable --disable-threads, for fftw3 show I also use --disable-threads? Wholley From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 11 March 2012 11:43 AM Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message On 11/03/2012 12:20 PM, Peter C. Lai wrote: Is fftw3 properly installed in /usr/local/lib? And of the right precision, like reading the installation guides will warn you... Mark On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote: Dear All, For Gromacs installation, my configure command is: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' --disable-threads. After make, the error message is as following. I am looking forward to getting a reply from you on how to avoid the error message. Wholly . .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined reference to `_fftwf_destroy_plan' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined references to `_fftwf_destroy_plan' follow .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined reference to `_fftwf_free' .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined reference to `_fftwf_free' collect2: ld returned 1 exit status Makefile:387: recipe for target `libmd.la' failed make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib' Makefile:302: recipe for target `all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:238: recipe for target `all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src' Makefile:347: recipe for target `all-recursive' failed make: *** [all-recursive] Error 1 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] genconf, grompp
Hi all When we want to fill a box containing for example 6 molecules we can not use genbox. We have to use genconf to build it. genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro When I use this command as I want a box including 6 molecules are filled When I open .gro file of the filled box I see the following format: Great Red Owns Many ACres of Sand 6 1DRGCAA1 0.495 -0.175 -0.072 0. 0. 0. 1DRGCAB2 0.483 -0.311 -0.143 0. 0. 0. 1DRGCAC3 0.388 -0.406 -0.069 0. 0. 0. 1DRGCAD4 0.451 -0.463 0.058 0. 0. 0. 1DRGCAE5 0.352 -0.557 0.127 0. 0. 0. 1DRGCAF6 0.415 -0.613 0.255 0. 0. 0. 2DRGCAA7 0.495 -0.175 -0.072 0. 0. 0. 2DRGCAB8 0.483 -0.311 -0.143 0. 0. 0. 2DRGCAC9 0.388 -0.406 -0.069 0. 0. 0. 2DRGCAD 10 0.451 -0.463 0.058 0. 0. 0. 2DRGCAE 11 0.352 -0.557 0.127 0. 0. 0. 2DRGCAF 12 0.415 -0.613 0.255 0. 0. 0. 3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0. 3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0. But when I want to minimise the simulation box and use grompp as the following: grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1 I receive the following error. Would you please help me? Thanks Saly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] genconf, grompp
Hi all When we want to fill a box containing for example 6 molecules we can not use genbox. We have to use genconf to build it. genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro When I use this command as I want a box including 6 molecules are filled When I open .gro file of the filled box I see the following format: Great Red Owns Many ACres of Sand 6 1DRGCAA1 0.495 -0.175 -0.072 0. 0. 0. 1DRGCAB2 0.483 -0.311 -0.143 0. 0. 0. 1DRGCAC3 0.388 -0.406 -0.069 0. 0. 0. 1DRGCAD4 0.451 -0.463 0.058 0. 0. 0. 1DRGCAE5 0.352 -0.557 0.127 0. 0. 0. 1DRGCAF6 0.415 -0.613 0.255 0. 0. 0. 2DRGCAA7 0.495 -0.175 -0.072 0. 0. 0. 2DRGCAB8 0.483 -0.311 -0.143 0. 0. 0. 2DRGCAC9 0.388 -0.406 -0.069 0. 0. 0. 2DRGCAD 10 0.451 -0.463 0.058 0. 0. 0. 2DRGCAE 11 0.352 -0.557 0.127 0. 0. 0. 2DRGCAF 12 0.415 -0.613 0.255 0. 0. 0. 3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0. 3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0. But when I want to minimise the simulation box and use grompp as the following: grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1 I receive the following error: -- - Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please help me? Thanks Saly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genconf, grompp
On 11/03/2012 2:50 PM, saly jackson wrote: Hi all When we want to fill a box containing for example 6 molecules we can not use genbox. We have to use genconf to build it. genconf -f H.gro -nbox 10 100 100 -o H-largebox.gro When I use this command as I want a box including 6 molecules are filled When I open .gro file of the filled box I see the following format: Great Red Owns Many ACres of Sand 6 1DRGCAA1 0.495 -0.175 -0.072 0. 0. 0. 1DRGCAB2 0.483 -0.311 -0.143 0. 0. 0. 1DRGCAC3 0.388 -0.406 -0.069 0. 0. 0. 1DRGCAD4 0.451 -0.463 0.058 0. 0. 0. 1DRGCAE5 0.352 -0.557 0.127 0. 0. 0. 1DRGCAF6 0.415 -0.613 0.255 0. 0. 0. 2DRGCAA7 0.495 -0.175 -0.072 0. 0. 0. 2DRGCAB8 0.483 -0.311 -0.143 0. 0. 0. 2DRGCAC9 0.388 -0.406 -0.069 0. 0. 0. 2DRGCAD 10 0.451 -0.463 0.058 0. 0. 0. 2DRGCAE 11 0.352 -0.557 0.127 0. 0. 0. 2DRGCAF 12 0.415 -0.613 0.255 0. 0. 0. 3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0. 3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0. But when I want to minimise the simulation box and use grompp as the following: grompp -f minim.mdp -c H-largebox.gro -p topol.top -o HMin.tpr -maxwarn 1 I receive the following error: -- - Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Would you please help me? You've been given all the help you can be given with the information you're giving us. See http://lists.gromacs.org/pipermail/gmx-users/2012-March/069235.html. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dist without output file
Dear Lina Very thanks for your time and attention. Initial command was : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5 After running following command the problem was solved : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 5 t: 17008 6773 NA 21881 NA 3.05534 (nm) t: 17008 6774 NA 21882 NA 3.27381 (nm) t: 17008 6775 NA 21883 NA 2.44312 (nm) t: 17008 6776 NA 21884 NA 2.0746 (nm) Last frame 2 time 17008.000 Now, I have a general question. In some of gromacs tools, there is distance parameter. I want to know what is dimension of the distance in gromacs? nm or A? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dist without output file
On 11/03/2012 6:38 PM, Atila Petrosian wrote: Dear Lina Very thanks for your time and attention. Initial command was : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5 After running following command the problem was solved : g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 5 t: 17008 6773 NA 21881 NA 3.05534 (nm) t: 17008 6774 NA 21882 NA 3.27381 (nm) t: 17008 6775 NA 21883 NA 2.44312 (nm) t: 17008 6776 NA 21884 NA 2.0746 (nm) Last frame 2 time 17008.000 Now, I have a general question. In some of gromacs tools, there is distance parameter. I want to know what is dimension of the distance in gromacs? nm or A? See manual section 2.2. Unfortunately, g_dist -dist is one of the places where the units are not redundantly specified in the g_dist -h help output. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
