[gmx-users] How to compile/run Gromacs on native Infiniband?
Dear all, My cluster has a FDR (56 Gb/s) Infiniband network. It is well known that there is a big difference between using IPoIB (IP over IB) with a normal sockets application and using native InfiniBand with an application that has been coded directly to the native IB verbs interface. The latter one gets much higher throughput and lower latency, while spending less CPU on networking. Therefore, I wonder if Gromacs has the native IB verbs interface. If so, how to compile and run Gromacs on native Infiniband? Any suggestions will be appreciated. Best Regards, Bert -- 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: mdrun did not support large file offsets
Dear all, When I compile gromacs using cmake, no large file related option was found in the cmake interface, however, I found the option for large file support in the CMakeCache.txt listed as bellow. . //Result of TEST_BIG_ENDIAN GMX_INTEGER_BIG_ENDIAN:INTERNAL=0 //Result of test for large file support GMX_LARGEFILES:INTERNAL=1 .. I wonder if GMX_LARGEFILES:INTERNAL=1 means that the it is OK for large file support in my cluster. If yes, why mdrun still tells to me that the large file offsets are not supported? Is there any way to make it work in my situation. Thanks for the reply. Best regards, Bo Dear gmx-users, When I continued a run on my x86_64 linux clusters using the command mdrun -deffnm prod -cpi prod.cpt -append, I got the errors as below: Program mdrun, VERSION 4.5.4 Source code file: checkpoint.c, line: 1734 Fatal error: The original run wrote a file called 'prod.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I also tried to recompile gromacs with alternative option --enable-largefile, but it still could not work. Then I compared the config.log generated using --enable-largefile and --disable-largefile (default) after configured, however, the two files were almost the same. How to solve this problem? Any suggestions are appreciated. Thanks in advance. Best regards, Bo -- 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] mdrun did not support large file offsets
Dear gmx-users, When I continued a run on my x86_64 linux clusters using the command mdrun -deffnm prod -cpi prod.cpt -append, I got the errors as below: Program mdrun, VERSION 4.5.4 Source code file: checkpoint.c, line: 1734 Fatal error: The original run wrote a file called 'prod.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I also tried to recompile gromacs with alternative option --enable-largefile, but it still could not work. Then I compared the config.log generated using --enable-largefile and --disable-largefile (default) after configured, however, the two files were almost the same. How to solve this problem? Any suggestions are appreciated. Thanks in advance. Best regards, Bo -- 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_hbond in 4.5.4 gives wrong output
Dear all, g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions are appreciated. Bests, Bert -- 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] How to compile the template.c when GMX is builded with cmake
Dear all, When GMX is builded with cmake, how to compile the template.c? I used to make the template.c by the command make -f MakefileXXX, but it can not work in version 4.5. Thanks for your suggestions. Best regards, Bert -- 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] Alternating electric fields in GROMACS
Dear all, I wonder if the alternating electric fields are implemented in the newly released GROMACS or somewhere, mayebe in the cvs code. If not, could someone give me a tip on how to do such revisions. Any suggestions are appreciated! As far as I know, it seems for a really long time that the manual says not implemented yet. Best regards, Bert -- 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] Question about Wall Potential
Dear gmx-users, I want to know the the specified form for the 10-4 wall potential in GROMACS. I assume it is: VLJ = C12*density*/z^10 - c6*density*/r^4 Am I right? If not, please correct me. Thanks for your suggestions in advance. Bests, Bert -- 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] absolute reference for pulling and center of mass removal
Dear gmx-users， I intend to pull a polymer in the bulk water using the pull code in gmx4. When I checked the manual, it was said With an absolute reference the system is no longer translation invariant and one should think about what to do with the center of mass motion. Yes, I set the pull group with the polymer and the reference group with the default (0,0,0). Then I received a warning after grompp as follows: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. I am not sure about the artifacts artifacts, could somebody give me a more definite explanation. Assuming we pull the COM of the polymer along x, and then the COM of water in x is coupled with that of the polymer, but the COM of water in yz is uncoupled. As a result, the momentum of system in yz could be nonzero for long time simulations if no COM removal is applied in yz. So to speak, if we do not remove the COM motion, artifacets could be induced by round errors in uncoupled yz direction. Am I right? How the deal with the COM removal in this case? I have done two tests here: 1) Set comm-grps = system. The polymer and the water flowed in the negative direction. 2) Set comm-grps = polymer SOL. The polymer still moved in x, and no COM motion observed for SOL. Which one could be appropriate, and if both are not ok, is there a way to solve the problems? Thanks for your suggestions in advance! Best regards, Bert -- 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] Error when compiled with fortran compiler in double precision
Dear gmx-users, An error was found when compiled gmx with fortran compiler in double precision, listed in the following: ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:141: error: 'nbkernel204_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:142: error: 'nbkernel210_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:143: error: 'nbkernel211_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:144: error: 'nbkernel212_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:145: error: 'nbkernel213_f77_double' undeclared here (not in a function) ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:146: error: 'nbkernel214_f77_double' undeclared here (not in a function) When I check the file nb_kernel_f77_double.c, the lines of inclusion were like this: #include nbkernel010_f77_double.h #include nbkernel020_f77_double.h #include nbkernel030_f77_double.h #include nbkernel100_f77_double.h #include nbkernel101_f77_double.h The naming of these header files are not consistent with the file name in dir nb_kernel_f77_double. Obviously an underline is lost here. I hope this issue will be fixed soon. Version: Gromacs-4.5b3 and the latest git vesion Command: configure --disable-float --enable-fortran ... Best Regards, Bert -- 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] Test suit failures
Dear gmx-users, I have done a test using test suit 4.0.4, and I got some failures as follows. All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 4 out of 14 complex tests FAILED FAILED. Check files in kernel020 FAILED. Check files in kernel120 FAILED. Check files in kernel121 FAILED. Check files in kernel122 FAILED. Check files in kernel123 FAILED. Check files in kernel124 FAILED. Check files in kernel220 FAILED. Check files in kernel221 FAILED. Check files in kernel222 FAILED. Check files in kernel223 FAILED. Check files in kernel224 FAILED. Check files in kernel320 FAILED. Check files in kernel321 FAILED. Check files in kernel322 FAILED. Check files in kernel323 FAILED. Check files in kernel324 16 out of 63 kernel tests FAILED All 45 pdb2gmx tests PASSED My gcc version is 4.1.1, and both gmx 4.0.4 and 4.0.5 get exactly the same failures on my Xeon 8 core based linux. For example, in /kernel/kernel020 checkpot.out gives: -- comparing energy file reference_s.edr and ener.edr There are 39 terms in the energy files There are 12 terms to compare in the energy files LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Files read succesfully -- checkvir.out gives: -- comparing energy file reference_s.edr and ener.edr There are 39 terms in the energy files There are 25 terms to compare in the energy files LJ-14step 0: -63.1209, step 0: 6.50742 Potentialstep 0: -321.601, step 0: -251.972 Kinetic En. step 0: 15.0135, step 0: 29.0739 Total Energy step 0: -306.588, step 0: -222.898 Temperature step 0: 1.93226, step 0: 3.74185 Pressure (bar) step 0: -3095.37, step 0: -2497.79 Vir-XX step 0: 1127.45, step 0: 1075.85 Vir-XY step 0:63.524, step 0: 21.7761 Vir-XZ step 0: -264.813, step 0: -260.354 Vir-YX step 0: 63.5241, step 0: 21.777 Vir-YY step 0: 803.252, step 0: 581.702 Vir-ZX step 0: -264.813, step 0: -260.354 Vir-ZZ step 0: 321.207, step 0: 176.573 Files read succesfully The deviations are obvious. Any suggestion would be appreciate. Thank you. Best Regards, Bert ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to make a soft repulsive potential wall
Hi gmx-users, I was simulating a water-surface system recently. The water molecules will escape from the solid surface, evaporate into the vacuum space above the surface, probably never come back and be trapped into the underpart of the surface for periodicity. I want to prevent the evaporating water molecules to be trapped by the lower part of the surface, and my thought is putting a soft repulsive potential wall just below the z_box. For clarity, the schematic is showed as follows, —— | vacuum| | | |×× wall ×× | (a soft repulsive potential wall ) | | | | | | | vacuum| |.| |water.| |.| |-| |-solid-| —— My questions are: 1) Note that wall function was is available in gmx4 now, I wonder which wall_type I should choose. I do not understand the phrase 'LJ integrated over the volume behind the wall' and 'LJ integrated over the wall surface, could you give me a little more explanation? 2) I test the both wall_types and each of them works fine (both walls are uncharged). I find that the LJ interation between the wall and the solid surface would not be cut-offed when the distance between them is beyond the vdw cutoff. I wonder if it is feasible that the water molecules will feel the repulsive force from the wall only within the cufoff distance around the wall. It would somewhat the same as the distance restraint, but the latter is hard to implement in intermolecular case. 3) If wall_type = table is used, could I set the dispersion columns to zero? Does rvdw work in this case? If you have any suggestions, that would be much appreciated. Thanks in advance. ___ 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] Walls user defined potential
Hi gmx-users and developers, I met a strange error when using wall function combined with user defined potential. Following is a part of the mdp: vdw-type = user energygrps = Surf SOL ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 2 wall_type= table wall_r_linpot= -1 wall_atomtype = W1 W2 wall_density= 1.5 1.5 wall_ewald_zfac = 2 energygrp_table = Surf wall0 Surf wall1 SOL wall0 SOL wall1 table-extension= 1.0 1) With the command bellow, mdrun -table table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod A fatal error was generated: Library file table_Surf_wall0_Surf_wall0.xvg not found in current dir nor in default directories. Then I copy the table6-12.xvg from the top dir, rename it by table.xvg and add it in the command line, mdrun -table table6-12.xvg table_Surf_wall0.xvg table_Surf_wall1.xvg table_SOL_wall0.xvg table_SOL_wall1.xvg -deffnm prod Am I right? It seems to be ok now. BTW, only the parameters in the replusive colunm in table_SOL_wall1.xvg are none zero (when z1, these values are aslo set to zero.) 2) But when I make a parallel run, a crash was found: One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 5798 failed on node n0 (127.0.0.1) due to signal 11. - mpirun failed with exit status 11 3) Moreover, if table-extension set to 0.0, a fatal error was caught: 'An atom is beyond the wall: coordinates -5371173273600.00 -20382570512384.00 2778490208256.00, distance -1.00 You might want to use the mdp option wall_r_linpot' I have tested several values, crash is found only when this value is less than 0.2. If you have any suggestions, that would be much appreciated. Thanks in advance. ___ 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: GMX 4.0 RC2: mdrun writes broken molecules?
I have encountered the same problem too. For water molecules not being broken in the mdrun, I think atoms in same charge group will not be divided into separate processors. It will be ok to use trjconv -pbc nojump/mol to get a clear visualization. Hi Justin, It's indeed the case that mdrun now writes broken molecules. Has to do with the domain decomposition and processors only keeping track of 'their' atoms. Too bad, but you'll just have to keep a .tpr around to make molecules whole again afterwards. Using trjconv -nojump with a suitable reference (not necessarily a .tpr) would also do it (and simultaneously remove the jumps...). Cheers, Tsjerk On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Hi, I've been running some simulations with Gromacs 4.0 RC2, and I've noticed something strange. In the output .gro file at the end of a run, the molecules in my system (a membrane protein) are broken, crossing periodic boundaries. This affects the lipids at the periphery of the box, in my case. Has there been some change since the previous version that mdrun is now writing broken molecules to fit everything within the unit cell? Or is this behavior unintentional? -Justin -- 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 constant defined in flexible TIP3P water model
Dear Gromacs Users, I have a simple question about the force constants of flexible TIP3P water model defined in Gromacs. From the literature (THE JOURNAL OF CHEMICAL PHYSICS 124, 024503 2006), the force constant for bond and angle is 1059.162 kcal/mol/angstrom^2 and 68.087 kcal/mol/rad^2, which is equivalent to 443153 kJ/mol/nm^2 and 285 kJ/mol/rad^2, respectively. These two values are inconsistent with the corresponding values in tip3p.itp, which gives 502416.0 kJ/mol/nm^2 for bond and 628.02 kJ/mol/rad^2 for angle. I wanna know which one will be ok to use. Thanks for your attention. Bert ___ 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] Crashes caused by particles communicated to PME node
Hi gmx-users, My system has a 7*7*22 box and 3dc geometry for PME is applid (large vacuum space is in the z direction. I found a crash caused by particles communicated to PME node. Note that this problem had a fix already ( http://www.gromacs.org/component/option,com_wrapper/Itemid,90/), I was afraid that it would not be fixed in PME3DC, because this problem did not occur when I shift to geometry=3d. Both 4.0rc1 and the latest CVS version had this error. Thanks for your suggestions. -output- Step 695, time 1.39 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.01, max 0.03 (between atoms 4610 and 4616) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4570 4576 30.60.1000 0.1000 0.1000 Step 696, time 1.392 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.01, max 0.04 (between atoms 4486 and 4492) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4570 4576 34.30.1000 0.1000 0.1000 Step 697, time 1.394 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.02, max 0.11 (between atoms 464 and 470) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 697, time 1.394 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.01, max 0.04 (between atoms 6586 and 6592) Step 697, time 1.394 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.01, max 0.03 (between atoms 3794 and 3800) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 697, time 1.394 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.01, max 0.04 (between atoms 5850 and 5856) 6038 6044 47.90.1000 0.1000 0.1000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4728 4734 30.90.1000 0.1000 0.1000 904910 58.90.1000 0.1000 0.1000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 697, time 1.394 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.248747, max 2.690606 (between atoms 3676 and 3682) 4570 4576 30.10.1000 0.1000 0.1000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3676 3682 90.00.1000 0.3691 0.1000 Wrote pdb files with previous and current coordinates --- Program mdrun, VERSION 4.0_rc1 Source code file: pme.c, line: 518 Fatal error: 2 particles communicated to PME node 2 are more than a cell length out of the domain decomposition cell of their charge group --- Wicky-wicky Wa-wild West (Will Smith) Error on node 2, will try to stop all the nodes Halting parallel program mdrun on CPU 2 out of 8 gcq#263: Wicky-wicky Wa-wild West (Will Smith) - One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 15418 failed on node n0 (127.0.0.1) with exit status 1. - ___ 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] PME 3dc geometry and the optimal PME mesh load
Hi all, I use 3dc geometry for a system with large box size in z direction, and when I try the new CVS version, I find a note saying The optimal PME mesh load is usually between 025 and 0.33, you should probably increase the cut-off and the PME grid spacing. A quite large estimation 0.86 was reported in grompp, and I wonder if I can do sth to speed up the simulation. Thanks for your suggestions in advance. ___ 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] analysizing the sam.edo script?
xi zhao wrote: Dear users: I want to analyze the EDS (essential dynamics sampling ) results (sam.edo file),though the website and manual both show that parse_edo can do it, I do not know how to get it,because I can not find it in the website. Please help me! I don't seem to have a local copy of parse_edo, but .edo files are ascii text files that can be readily parsed with standard tools like awk. Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ 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: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue
sunita gupta wrote: Hello I have a query that how to do PCA which further includes *plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue*. I read in many articles that this can be done using gromacs. I did my MD simutaion using charmm forcefield and NAMD. I have converted my *dcd file trr* and using *g_covar *covariance analysis. But i am not getting anything regarding displacement calculation In GROMACS 3.1 manual their is an option of *-disp* is given with *g_anaeig* command...but in 3.2 and 3.3. no such information is given and its considering as invalid argument. Also someone mailed me that calculating the displacement along eigenvectors is same as rmsf (root mean square fluctuation) and it can be calculated using -rmsf option in g_anaeig commant..Kindly help me in this regard and clear my doubts... g_anaeig -rmsf seems a perfectly valid suggestion to me. What's your doubt? Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ 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] query about .xpm file
Hi gmx-usrs, I use the program g_densmap to generate a xpm file, and then I convert it to eps format with xpm2ps. It goes quite well except for the illegible coordinates with the ticks. I wonder if I can set those coodinates arbitrarily. I have tried to adjust the -bx, -by set and the m2p input file, but I can not set the coordinates of the ticks with regular integers. Thanks very much for suggestions. Bert ___ 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: gmx-users Digest, Vol 48, Issue 24
Thanks David. There still inconsitent shifts warnings with a tpr made by pbc=xyz. By the way, my itp file is not changed, that is, the bonded terms between periodic images are still in the topology. Should I make a topology with pbc=xyz too? Bert wrote: Hi all, I use pbc=full in my system, and all runs are ok except for the inconsistent shifts warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with consideration of full pbc. Am I right? If so, how to deal with these warnings? Thanks in advance. make a tpr with pbc=xyz for analysis. ___ 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. 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] inconsistent shifts
Hi all, I use pbc=full in my system, and all runs are ok except for the inconsistent shifts warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with consideration of full pbc. Am I right? If so, how to deal with these warnings? Thanks in advance. ___ 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] normal mode analysis
Robert Fenwick wrote: Hi, I am interested in comparing the normal modes of a protein with and without a ligand. I have already computed the lowest 100 normal modes for the protein (eigenvec_a.trr) and the protein:ligand complex and have reduced the protein:ligand eigenvec_b.trr to the protein by issuing; trjconv_d -f eigenvec_b.trr -o eigenvec_c.trr -s nm_a.tpr select 0 [System] Where: + nm_a.tpr is the tpr file of the protein alone + eigenvec_b.trr is the trajectory of the protein:ligand + eigenvec_c.trr is the new trajectory of the complex minus the ligand coordinates What I want to do now is compare the eigenvec_a.trr and eigenvec_c.trr files to see the mode overlap between the free and bound protein. What I can not understand how to remove the effects of rotation and translation of the protein with respect to the ligand that will be present in the eigenvec_c.trr. Is it possible to do this type of analysis in GROMACS and how can I go about it? if you remove part of the system e.g. the ligand) from a set of eigenvectors you'll end up with non-orthogonal vectors. This is almost certainly not what you want. I'd suggest for each set of normal modes (with and without ligand) to generate a corresponding ensemble at a certain temperature with g_nmens. Then from those trajectories you can cut out the ligand to generate two protein-only trajectories, on which you then can run a PCA with g_covar (either separately and calculate eigenvector overlaps, or concatenate both trajectories and look at projection differences). best, Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ 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] Reading XTC files from fortran90
On Sat, 29 Sep 2007, Jones de Andrade wrote: Hi Bert. Thank you for the prompt answer. Just did as instructed, but got the following: CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c IPO link: can not find -lxrdf well, apparently the path you specify with -L does not contain a libxdrf.a the way you called it the compiler expects it to be located here: /home/johannes/src/own/B/9/xtc/xtc/libxdrf.a also, IIRC, the xtcio stuff is already linked into the libxdrf.a, so no need to include it again. ifort: error: problem during multi-file optimization compilation (code 1) Looks better, in the sense that the number of error messages was reduced. But still doesn't accept to link to the xrdf library. Tried that with and without re-make of the library (strange fact that the SGI arch is to be used in linux) and also tried to say -llibxrdf instead of -lxrdf. Nothing worked. Have you or someone come across such an error before? Any clue of what can possibly be going wrong? Thanks a lot in advance... Sincerally yours, Jones On 9/29/07, Bert de Groot [EMAIL PROTECTED] wrote: Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know what happens if you readwrite from the same file. Bert Bert Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.gwdg.de/groups/de_groot ___ 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] Reading XTC files from fortran90
Hi, try: download http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz (and optionally issue a 'make' in the xtc directory after unpacking) in the linking stage, use something like ifort -blabla -lxdrf -L/wherever/xtc -lg2c your smalll test code looks OK apart from the fact that I don't know what happens if you readwrite from the same file. Bert On Sat, 29 Sep 2007, Jones de Andrade wrote: Hi all. I'm writing this beucase I'm having terrible problems in trying to deal with gromacs trajectory files with my own programs, originally written on fortran90. The codes themselves are enoughly big to make it out of question to try to translate them. What leads to some sort of mixed language compilation. My first guess was to try to use the guidelines from http://xray.bmc.uu.se/~spoel/md/online/xtc.html, but it absolutelly didn't worked. Could not find a compatible library. Tried to recompile gromacs in order to do so, but instead of a libsdrf.a library file, it created just common .lo and .o object files. Looked inside concoord program, as there are some mentions in the list to look at the code. Was a really good aprentize, could understand better the logics involved when dealing with .xtc files, BUT I could not use the library files that came with that. Somehow, it wasn't recognized as a valid file. My last try up to now was to try to link my test-read-program with the libxdrf object file. It yelded the following error: CruNumMac src/own/B/9/xtc 238% ifort libxdrf.lo xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.lo; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifortZNvZHh.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifortZNvZHh.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. libxdrf.lo: file not recognized: File format not recognized If I try to link to the .o objetc: CruNumMac src/own/B/9/xtc 240% ifort libxdrf.o xtciof.f90 test_xtc.f90 IPO: WARNING: no IR in object file libxdrf.o; was the source file compiled with -ipo? IPO Error: unresolved : xdrfint_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfclose_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrfopen_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrffloat_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : xdrf3dfcoord_ Referenced in /tmp/ipo_ifort2f5KMw.o IPO Error: unresolved : ffclose Referenced in libxdrf.o IPO: performing multi-file optimizations IPO: generating object file /tmp/ipo_ifort2f5KMw.o test_xtc.f90(17) : (col. 3) remark: LOOP WAS VECTORIZED. test_xtc.f90(25) : (col. 8) remark: LOOP WAS VECTORIZED. xtciof.f90(112) : (col. 3) remark: LOOP WAS VECTORIZED. /tmp/ipo_ifort2f5KMw.o(.text+0x1e1): In function `MAIN__': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x4ea):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x517):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x92b): In function `xtciof_mp_xtcheader_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x941):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x95e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfint_' /tmp/ipo_ifort2f5KMw.o(.text+0x97b):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xb8e): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xbde):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc2e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xc7e):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrffloat_' /tmp/ipo_ifort2f5KMw.o(.text+0xcce):/tmp/ipo_ifort2f5KMw.f: more undefined references to `xdrffloat_' follow /tmp/ipo_ifort2f5KMw.o(.text+0xe6b): In function `xtciof_mp_xtcio_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrf3dfcoord_' /tmp/ipo_ifort2f5KMw.o(.text+0xfc6): In function `xtciof_mp_xtcopen_': /tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfopen_' /tmp/ipo_ifort2f5KMw.o(.text+0x1292):/tmp/ipo_ifort2f5KMw.f: undefined reference to `xdrfclose_' /tmp/ipo_ifort2f5KMw.o(.text+0x12b3):/tmp
Re: [gmx-users] Doubt about -linfix, -linacc, -radfix, -radacc, -radcon
-- Anirban Ghosh wrote: Hi All, I want to perform ED sampling along first principle component in GROMACS. For that I am using the make_edi command to generate the required .edi file to be subsequently used in mdrun. But I cannot understand the meaning of the algorithms -linfix, -linacc, -radfix, -radacc and -radcon. What does fixed step linear expansion and fixed step radius expansion specify here? as make_edi -h says: -linfix: perform fixed-step linear expansion along selected eigenvectors. -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). -radfix: perform fixed-step radius expansion along selected eigenvectors. -radacc: perform acceptance radius expansion along selected eigenvectors. (steps in the desired direction will be accepted, others will be rejected). Note: by default the starting MD structure will be taken as origin of the first expansion cycle for radius expansion. If -ori is specified, you will be able to read in a structure file that defines an external origin. -radcon: perform acceptance radius contraction along selected eigenvectors towards a target structure specified with -tar.NOTE: each eigenvector can be selected only once. If you only want to constrain the position along the first eigenvector, linfix and linacc are probably the most meaningful options. With -linfix, you impose a predefined fixed stepsize per MD step (specified with -linstep). In that case, you could use something like: make_edi -f -s -n -linfix 1 -linstep -0.0001 Using -linacc, you don't specify a fixed stepsize, but let the MD decide the stepsize. The only constraint that is applied in that case that (if you choose the forward direction as target) that backward steps are prohibited. In that case, use something like: make_edi -f -s -n -linfix 1 -accdir 1.0 (here the positive sign of the accdir argument specifies the direction). How should I give the string options for these algorithms see example above and which one should I use? that we cannot answer for you. It all depends on the question you're trying to address with these simulations. Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ 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] rotational fit in XY plane only
Berk Hess wrote: From: Dr Itamar Kass [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] rotational fit in XY plane only Date: Wed, 02 May 2007 19:44:12 +0800 Hi all, I study a protein which is moving toward an interface during my simulation. In order to analyse the why the protein is bound to the interface I want to fit all my results. There is no problem with translational fit, but I want to do rotational fit only in the XY plane. Is there a nice way of doing so? Best, Itamar Currently there is not. I would like to have that feature as well. can't you simply set all z-coordinates to zero and carry out a 3D fit as usual? (you may get a problem with mirror images, but the handedness is anyway not anymore uniquely defined once you project on 2D). Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ 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] Essential Dynamics Sampling (EDS) MD
Ran Friedman wrote:
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
The Jacobi error hints at a fitting problem. If not the starting position,
could it
be the target that's causing the problems?
Please check the head of the .edo and log files, to see if the reported RMSD's
are what you would expect and especially if reported projections are compatible
with
g_anaeig.
Large VCM(group rest): nan, nan, nan,
ekin-cm: nan
In the log file.
Ran.
Lars Schaefer wrote:
Dear Ran,
this could mean that you have problems fitting to your reference
structure.
Lars
Ran Friedman wrote:
Dear all,
I'm resending this message (please see below) with some additional
info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -debug flag and got some nan values in
mdrun.log:
dekin = nan, ekin = 175815 vcm = ( nan nan nan)
mv = ( nan nan nan)
PC: pres (3x3):
PC: pres[0]={ nan, nan, nan}
PC: pres[1]={ nan, nan, nan}
PC: pres[2]={ nan, nan, nan}
PC: ekin (3x3):
PC: ekin[0]={ nan, nan, nan}
PC: ekin[1]={ nan, nan, nan}
PC: ekin[2]={ nan, nan, nan}
PC: vir (3x3):
PC: vir [0]={ 5.66646e+04, 1.12632e+02, -1.88577e+03}
PC: vir [1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03}
PC: vir [2]={-1.82055e+03, 3.43891e+03, 6.20980e+04}
PC: box (3x3):
PC: box [0]={ 9.73688e+00, 0.0e+00, 0.0e+00}
PC: box [1]={ 3.24470e+00, 9.11683e+00, 0.0e+00}
PC: box [2]={-3.24470e+00, 4.55842e+00, 7.97596e+00}
fshift after SR (27x3):
fshift after SR[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[3]={ nan, nan, nan}
fshift after SR[4]={ nan, nan, nan}
What am I missing?
Ran Friedman wrote:
Dear all,
I'm trying to run MD with ED sampling. The target structure is a
protein
taken from one simulation, the .tpr file is taken from a different one.
I'm using a subset of the CA atoms to calculate the eigenvectors. The
problem is that the MD run crashes after set-up.
Depending on the machine, it either crashes without any error
message or
complains about Too many iterations in routine JACOBI.
Any suggestions?
Thanks,
Ran.
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--
Bert
__
Bert de Groot, PhD
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany
tel: +49-551-2012308, fax: +49-551-2012302
http://www.mpibpc.mpg.de/groups/de_groot
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Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Ran Friedman wrote: Dear Bert, The Jacobi error hints at a fitting problem. If not the starting position, could it be the target that's causing the problems? Please check the head of the .edo and log files, to see if the reported RMSD's are what you would expect and especially if reported projections are compatible with g_anaeig. Do you refer to EDx? The values are not equal to what I get from g_anaeig. then there's possibly some mixup between fitting reference and/or selection and/or the eigenvectors between g_anaeig and make_edi? Please make sure that group selections and reference groups (-s option of make_edi, g_covar and g_anaeig) are identical. Check covar.log if you're not sure anymore which fitting structure/selection you chose for g_covar. If you still have problems, please feel free to contact me off-list with a minimal set of files with which the problem can be reproduced. cheers, Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
