[gmx-users] problem in energy minimisation to allow only hydrogen molecule to relax
Dear all I have to apply only Hydrogen molecule will be relax during energy minimization of protein molecule. can anyone have idea about what short of changes I have to make in em.mdp file to allow only hydrogen molecule is relaxable during energy minimisation? my em.mdp file like this- Thanks a lot in advance. Nitu sharma. ___ 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] problem during energy minimisation to allow only hydrogen molecule to relax
Dear all I have to apply only Hydrogen molecule will be relax during energy minimization of protein molecule. can anyone have idea about what short of changes I have to make in em.mdp file to allow only hydrogen molecule is relaxable during energy minimisation? my em.mdp file like this- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.001 nsteps = 100 ; ; Energy minimizing stuff ; emtol = 10 emstep = 0.01 nstcgsteep = 1000 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Thanks a lot in advance. Nitu sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] changing pdb file residue name
Hi Rukmani Sridharan, It's not a matter of name. Gromacs is unlikely to have a topological description of the molecule and you have to provide that. See http://oldwiki.gromacs.org/index.php/Parameterization Cheers, Tsjerk On Mon, Jul 6, 2009 at 6:06 AM, Rukmani Sridharanrukmani.grom...@gmail.com wrote: Hi, I am a bit new to gromacs and am familiarizing myself with the various commands. I want to simulate an unusual molecule, with the formula C7H10. The downloaded pdb file had the residue mname MON which gromacs does not recognize. How should i name the residue? ___ gmx-users mailing list gmx-us...@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 -- 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem during energy minimisation to allow only hydrogen molecule to relax
you could use position restrains on the other atoms (non hydrogens) or use freezing groups. it seems that your system has a major problem: bad contacts ... check it prior to EM. On Jul 6, 2009, at 8:30 AM, nitu sharma wrote: Dear all I have to apply only Hydrogen molecule will be relax during energy minimization of protein molecule. can anyone have idea about what short of changes I have to make in em.mdp file to allow only hydrogen molecule is relaxable during energy minimisation? my em.mdp file like this- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.001 nsteps = 100 ; ; Energy minimizing stuff ; emtol = 10 emstep = 0.01 nstcgsteep = 1000 nstcomm = 1 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 vdw-type= cut-off rvdw= 1.0 coulombtype = PME Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ Thanks a lot in advance. Nitu sharma. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] WG: Changing of pulling paramters during simulation
Hi, short question: can one change the pulling parameters e.gin the afm modus during the simulation (vector and or force) Hans HEINDL University of Westminster School of Biosciences ___ 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] Buffer overflow on Fedora 10
I have an odd problem running the Gromacs 4.0.4 RPM installable as part of Fedora 10. On two machines, it runs fine. On a third, each program I invoke dies as a result of the buffer overflow detector in glibc. Here's some example output: g_mdrun :-) G R O M A C S (-: *** buffer overflow detected ***: g_mdrun terminated === Backtrace: = /lib64/libc.so.6(__fortify_fail+0x37)[0x3a400ff4c7] /lib64/libc.so.6[0x3a400fd370] /lib64/libc.so.6[0x3a400fc15d] /usr/lib64/libgmx.so.5(get_libdir+0x23f)[0x7fb3ac50e22f] /usr/lib64/libgmx.so.5(low_libfn+0x1b4)[0x7fb3ac50e454] /usr/lib64/libgmx.so.5(low_libopen+0x15)[0x7fb3ac50e4c5] /usr/lib64/libgmx.so.5[0x7fb3ac5046d9] /usr/lib64/libgmx.so.5(bromacs+0x21)[0x7fb3ac504931] /usr/lib64/libgmx.so.5(CopyRight+0x59)[0x7fb3ac504999] g_mdrun[0x4153b7] /lib64/libc.so.6(__libc_start_main+0xe6)[0x3a4001e576] g_mdrun[0x404539] === Memory map: 0040-0041f000 r-xp fd:02 2723129 /usr/bin/g_mdrun 0061f000-00621000 rw-p 0001f000 fd:02 2723129 /usr/bin/g_mdrun 025c9000-025ea000 rw-p 025c9000 00:00 0 [heap] 3a3ec0-3a3ec2 r-xp 08:06 1114115 /lib64/ld-2.9.so 3a3ee1f000-3a3ee2 r--p 0001f000 08:06 1114115 /lib64/ld-2.9.so 3a3ee2-3a3ee21000 rw-p 0002 08:06 1114115 /lib64/ld-2.9.so 3a3f00-3a3f0f1000 r-xp fd:02 2426042 /usr/lib64/libfftw3f.so.3.2.3 3a3f0f1000-3a3f2f1000 ---p 000f1000 fd:02 2426042 /usr/lib64/libfftw3f.so.3.2.3 3a3f2f1000-3a3f2f8000 rw-p 000f1000 fd:02 2426042 /usr/lib64/libfftw3f.so.3.2.3 3a4000-3a40168000 r-xp 08:06 1114117 /lib64/libc-2.9.so 3a40168000-3a40368000 ---p 00168000 08:06 1114117 /lib64/libc-2.9.so 3a40368000-3a4036c000 r--p 00168000 08:06 1114117 /lib64/libc-2.9.so 3a4036c000-3a4036d000 rw-p 0016c000 08:06 1114117 /lib64/libc-2.9.so 3a4036d000-3a40372000 rw-p 3a4036d000 00:00 0 3a4040-3a40484000 r-xp 08:06 1114123 /lib64/libm-2.9.so 3a40484000-3a40683000 ---p 00084000 08:06 1114123 /lib64/libm-2.9.so 3a40683000-3a40684000 r--p 00083000 08:06 1114123 /lib64/libm-2.9.so 3a40684000-3a40685000 rw-p 00084000 08:06 1114123 /lib64/libm-2.9.so 3a4080-3a40802000 r-xp 08:06 1114125 /lib64/libdl-2.9.so 3a40802000-3a40a02000 ---p 2000 08:06 1114125 /lib64/libdl-2.9.so 3a40a02000-3a40a03000 r--p 2000 08:06 1114125 /lib64/libdl-2.9.so 3a40a03000-3a40a04000 rw-p 3000 08:06 1114125 /lib64/libdl-2.9.so 3a40c0-3a40c17000 r-xp 08:06 1114136 /lib64/libpthread-2.9.so 3a40c17000-3a40e16000 ---p 00017000 08:06 1114136 /lib64/libpthread-2.9.so 3a40e16000-3a40e17000 r--p 00016000 08:06 1114136 /lib64/libpthread-2.9.so 3a40e17000-3a40e18000 rw-p 00017000 08:06 1114136 /lib64/libpthread-2.9.so 3a40e18000-3a40e1c000 rw-p 3a40e18000 00:00 0 3a4100-3a41015000 r-xp 08:06 1114139 /lib64/libz.so.1.2.3 3a41015000-3a41214000 ---p 00015000 08:06 1114139 /lib64/libz.so.1.2.3 3a41214000-3a41215000 rw-p 00014000 08:06 1114139 /lib64/libz.so.1.2.3 3a4180-3a41802000 r-xp fd:02 2425045 /usr/lib64/libXau.so.6.0.0 3a41802000-3a41a01000 ---p 2000 fd:02 2425045 /usr/lib64/libXau.so.6.0.0 3a41a01000-3a41a02000 rw-p 1000 fd:02 2425045 /usr/lib64/libXau.so.6.0.0 3a41c0-3a41c05000 r-xp fd:02 2425032 /usr/lib64/libXdmcp.so.6.0.0 3a41c05000-3a41e04000 ---p 5000 fd:02 2425032 /usr/lib64/libXdmcp.so.6.0.0 3a41e04000-3a41e05000 rw-p 4000 fd:02 2425032 /usr/lib64/libXdmcp.so.6.0.0 3a4200-3a42105000 r-xp fd:02 2425062 /usr/lib64/libX11.so.6.2.0 3a42105000-3a42305000 ---p 00105000 fd:02 2425062 /usr/lib64/libX11.so.6.2.0 3a42305000-3a4230b000 rw-p 00105000 fd:02 2425062 /usr/lib64/libX11.so.6.2.0 3a4340-3a43403000 r-xp 08:06 1114147 /lib64/libuuid.so.1.2 3a43403000-3a43603000 ---p 3000 08:06 1114147 /lib64/libuuid.so.1.2 3a43603000-3a43604000 rw-p 3000 08:06 1114147 /lib64/libuuid.so.1.2 3a4380-3a43817000 r-xp fd:02 2425041 /usr/lib64/libICE.so.6.3.0
Re: [gmx-users] Buffer overflow on Fedora 10
On Mon, 2009-07-06 at 11:18 +0100, Adam Huffman wrote: I have an odd problem running the Gromacs 4.0.4 RPM installable as part of Fedora 10. On two machines, it runs fine. On a third, each program I invoke dies as a result of the buffer overflow detector in glibc. Here's some example output: The same thing happens if I recompile the SRPM myself and install that. Any clues as to how to track this down would be greatly appreciated. Install the debuginfo with # debuginfo-install gromacs and run gromacs with gdb: $ gdb g_mdrun (gdb) run -s topol.tpr (and so on.) Gdb might tell you to install the debuginfo of other packages too. I have been working on getting also debug binaries in the package, but I won't push the new package until 4.0.6 is released which fixes the build error on ppc64 architecture. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Buffer overflow on Fedora 10
Jussi Lehtola wrote: On Mon, 2009-07-06 at 11:18 +0100, Adam Huffman wrote: I have an odd problem running the Gromacs 4.0.4 RPM installable as part of Fedora 10. On two machines, it runs fine. On a third, each program I invoke dies as a result of the buffer overflow detector in glibc. Here's some example output: The same thing happens if I recompile the SRPM myself and install that. Any clues as to how to track this down would be greatly appreciated. Install the debuginfo with # debuginfo-install gromacs and run gromacs with gdb: $ gdb g_mdrun (gdb) run -s topol.tpr (and so on.) Gdb might tell you to install the debuginfo of other packages too. I have been working on getting also debug binaries in the package, but I won't push the new package until 4.0.6 is released which fixes the build error on ppc64 architecture. I've installed several debuginfo packages and when run via gdb the crash doesn't occur...: (gdb) r Starting program: /usr/bin/g_mdrun warning: /usr/lib/debug/usr/lib64/atlas/libblas.so.3.0.debug: The separate debug info file has no debug info warning: /usr/lib/debug/usr/lib64/atlas/liblapack.so.3.0.debug: The separate debug info file has no debug info [Thread debugging using libthread_db enabled] then the usage message and Program exited with code 0377. ___ 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] MdRun Crash
hi, I am running a simulation of a membrane protein in DPPC bilayer. ii have completed upto genion step. But when i am going to minimize the energy of the system the mdrun crashes showing Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 10. Potential Energy = -9.8290938e+21 Maximum force = 6.7779973e+24 on atom 5591 Norm of force = 2.4384918e+22 i can understand the problem lies in the mdp file used, i.e. in the Epot and Fmax. i have rerun the step using different values but with same result.please suggest me how to overcome the constraints problem. thanking you in advance. mdp file is here integrator = steep emstep = 0.001 emtol = 1000 nsteps = 5000 nstlist = 1 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc = xyz Shamik Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Buffer overflow on Fedora 10
On Mon, 2009-07-06 at 11:37 +0100, Adam Huffman wrote: I've installed several debuginfo packages and when run via gdb the crash doesn't occur...: (gdb) r Starting program: /usr/bin/g_mdrun warning: /usr/lib/debug/usr/lib64/atlas/libblas.so.3.0.debug: The separate debug info file has no debug info warning: /usr/lib/debug/usr/lib64/atlas/liblapack.so.3.0.debug: The separate debug info file has no debug info [Thread debugging using libthread_db enabled] then the usage message and When I run $ gdb g_mdrun (gdb) r I get (clip) Program g_mdrun, VERSION 4.0.4 Source code file: ../../../src/gmxlib/gmxfio.c, line: 736 Can not open file: topol.tpr (clip) Program exited with code 0377. Instead of running $ gdb g_mdrun [mdrun options] (gdb) run you need to run $ gdb g_mdrun (gdb) run [mdrun options] -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Buffer overflow on Fedora 10
Jussi Lehtola wrote: On Mon, 2009-07-06 at 11:37 +0100, Adam Huffman wrote: I've installed several debuginfo packages and when run via gdb the crash doesn't occur...: (gdb) r Starting program: /usr/bin/g_mdrun warning: /usr/lib/debug/usr/lib64/atlas/libblas.so.3.0.debug: The separate debug info file has no debug info warning: /usr/lib/debug/usr/lib64/atlas/liblapack.so.3.0.debug: The separate debug info file has no debug info [Thread debugging using libthread_db enabled] then the usage message and When I run $ gdb g_mdrun (gdb) r I get (clip) Program g_mdrun, VERSION 4.0.4 Source code file: ../../../src/gmxlib/gmxfio.c, line: 736 Can not open file: topol.tpr (clip) Program exited with code 0377. Yes, I see that. At this stage, I just want the program to start without crashing. At the moment it crashes even without trying to load any input files, but not when run under gdb. Instead of running $ gdb g_mdrun [mdrun options] (gdb) run you need to run $ gdb g_mdrun (gdb) run [mdrun options] ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Buffer overflow on Fedora 10
Adam Huffman wrote: Jussi Lehtola wrote: On Mon, 2009-07-06 at 11:37 +0100, Adam Huffman wrote: I've installed several debuginfo packages and when run via gdb the crash doesn't occur...: (gdb) r Starting program: /usr/bin/g_mdrun warning: /usr/lib/debug/usr/lib64/atlas/libblas.so.3.0.debug: The separate debug info file has no debug info warning: /usr/lib/debug/usr/lib64/atlas/liblapack.so.3.0.debug: The separate debug info file has no debug info [Thread debugging using libthread_db enabled] then the usage message and When I run $ gdb g_mdrun (gdb) r I get (clip) Program g_mdrun, VERSION 4.0.4 Source code file: ../../../src/gmxlib/gmxfio.c, line: 736 Can not open file: topol.tpr (clip) Program exited with code 0377. Yes, I see that. At this stage, I just want the program to start without crashing. At the moment it crashes even without trying to load any input files, but not when run under gdb. If you are adventurous you could try to run it through valgrind which will spot memory errors. valgrind mdrun [ options ] You may need to install the valgrind program. Instead of running $ gdb g_mdrun [mdrun options] (gdb) run you need to run $ gdb g_mdrun (gdb) run [mdrun options] ___ 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Shift electrostatic summation
Dear all, I was trying to modify the Shift option of electrostatic summation. Mainly I want to modify the formulas of this electrostatic summation. From the manual page 69, the modified non-bonded interactions, the formulas about Shift is there. In the file /src/gmxlib/shift_util.c, there are these formulas. So is this the only file for Shift? Since I have added some printf lines to this file, I do not see the result when I recompile and use Shift. I doubt whether this function was called to do Shift. Or is there any other file related with the Shift method and I need to change? Thanks in advance. -- Shuangxing Dai ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] False C6/C12 parameter for DMSO and chloroform in GROMOS 45a3 force field (ffG45a3)
Roman Affentranger schrieb: Dear gmx-users (and developers ;-) I believe there are false LJ pair-parameters in gromacs' implementation of the GROMOS 45a3 force field for interactions between the atoms of DMSO, and between the atoms of chloroform. The C6/C12 pair paramteters for CDMSO-SDMSO, ODMSO-SDMSO, ODMSO-CDMSO, and CLCHL-CCHL, HCHL-CCHL, HCHL-CLCHL in ffG45a3nb.itp are simply the (root of the) product of the individual atomic parameters, whereas separate parameters - with no relation to the atomic ones - are defined in the original GROMOS force field. Hi Roman, I think there actually is a relation of the pair parameters to the individual atomic parameters in G43a1 as well as in G45a3 since all of the values are based on the same epsilon and sigma numbers. (For DMSO: epsilon = 1.297 kJ/mol for S, 1.7154 for O, 0.9414 for CH3 sigma = 0.356 nm for S, 0.263 for O, 0.366 for CH3) The difference in the C6/C12 pair parameters apparently is due to the use of different combination rules (see GROMACSmanual-4.0.pdf, chapter 5.3.3). For G45a3 equations (5.1) and (5.3) are used to calculate the respective pair parameters, whereas for G43a1 eq. (5.4) and after that (5.1) are used. So I guess the question is, which is the right way for the combination? Cheers, Markus The errors are there in the force field files distributed with gromacs version 4.0.5 all the way down to at least version 3.2.1 (it's as far as I've looked), and also in the ffG45a3.tar.gz file to be found at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields For example: The lines in ffG45a3nb.itp read: CDMSOSDMSO 1 0.009777435 2.1627421e-05 ... ODMSOSDMSO 1 0.004897196 4.0192831e-06 ODMSOCDMSO 1 0.0045335636 4.0434685e-06 However, they should be CDMSOSDMSO 1 0.0097827 2.16523e-05 ... ODMSOSDMSO 1 0.0052442 4.6094e-06 ODMSOCDMSO 1 0.0049187 4.7597e-06 as they are in the GROMOS 43a1 force field. A similar problem holds for chloroform (atoms CCHL, CLCHL and HCHL). Find attached a corrected version of ffG45a3nb.itp. Cheers, Roman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trouble with a triple bond
Thanks for the help, I think it worked out. Just for the record: For my chain-like molecule ...- C17 - C18 # C19 - C20 - ... (# = triple bond) I defined C18 and C19 to be virtual sites defined by the positions of C17 and C20: [ virtual_sites2 ] ; Site from funct a 18 17 20 1 0.353365385 19 17 20 1 0.646634615 And constrained the distance between C17 and C20 to be the sum of the three original bonds shown above: [ constraints ] ; index1 index2 funct length(nm) 17 20 1 0.416 However, I had to set the mass of the non-virtual particles C18 and C19 to zero, as Gromacs demands virtual sites have no mass. So technically speaking, my molecule has lost weight. I hope that doesn't lead to artefacts, but as of now trajectories are looking good. Regards, Alex Maybe this previous post will be of some use: http://lists.gromacs.org/pipermail/gmx-users/2009-May/042068.html -Justin Alexander Bujotzek wrote: Dear all, I am experiencing some trouble with a small molecule containing a C-C triple bond, using a topology built by PRODRG beta. I intend to use ffG43a2, with a contraint on all bond lengths. Energy minization does not converge, as forces on the atoms involved in the bond seem to oscillate (not very high forces, though). Position restrained MD fails with LINCS errors, and unrestrained MD leads to a blow-up of the system. I guess the fault lies in the representation of the triple bond in the topology file, as a derivate of the molecule (with a single bond in the same place) works just fine. Excerpt from the itp building block provided by PRODRG beta. The triple bond is supposed to be between carbons 18 and 19: [ bonds ] ... 17 18 20.147 3422818.40.147 3422818.4 ; CAQ CAR 18 19 20.122 2309822.80.122 2309822.8 ; CAR CAS20 19 20.147 3422818.40.147 3422818.4 ; CAT CAS ... [ angles ] ... 16 17 18 2109.5 520.0109.5 520.0 ; OAP CAQ CAR 17 18 19 2180.0 41840001.2180.0 41840001.2 ; CAQ CAR CAS 18 19 20 2180.0 41840001.2180.0 41840001.2 ; CAR CAS CAT 19 20 21 2109.5 520.0109.5 520.0 ; CAS CAT OAU ... There is no dihedral with 18 and 19 in the middle, but I assume that is correct as triple bonds are not supposed to be rotatable? What strikes me is the high force constant on the two 180 degree angles... may that be a source of error? Any help is appreciated! Maybe someone even has a working template of a correct triple bond topology at hand? Best regards and thank you for reading Alex PS: I also checked ffG43a2bon.itp, but I found nothing resembling a C-C triple bond... or maybe it's just the heat in my office. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Alexander Bujotzek Zuse Institute Berlin Computational Drug Design Group Tel. : +49 30 84185-234 eMail: bujot...@zib.de ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] False C6/C12 parameter for DMSO and chloroform in GROMOS 45a3 force field (ffG45a3)
Hi Markus I can not quite follow your arguments. The original publication on the GROMOS96 43a1 force field (W.F. van Gunsteren et al., Biomolecular Simulation: The GROMOS96 manual and user guide, Hochschulverlag AG an der ETH Zürich, 1996, Zürich, Switzerland) explicitly gives the pair parameters for interactions between non-equal atom types of DMSO (and of chloroform). See table 2.5.6.2.6 of the mentioned book. ffG43a1nb.itp actually contains these values. ffG45a3nb.itp contains the pair parameter one would obtain from the atomic parameters using eq. 5.3 in the GROMACS 4.0 manual. So the question is not so much which one is the right combination rule, since the pair parameter are given explicitly in the original reference of the GROMOS96 43a1 force field, and the values of DMSO (and chloroform) have not been reparametrized for the 45a3 force field. Cheers, Roman On Mon, Jul 6, 2009 at 5:07 PM, Markus Tusch mtu...@mail.upb.de wrote: Roman Affentranger schrieb: Dear gmx-users (and developers ;-) I believe there are false LJ pair-parameters in gromacs' implementation of the GROMOS 45a3 force field for interactions between the atoms of DMSO, and between the atoms of chloroform. The C6/C12 pair paramteters for CDMSO-SDMSO, ODMSO-SDMSO, ODMSO-CDMSO, and CLCHL-CCHL, HCHL-CCHL, HCHL-CLCHL in ffG45a3nb.itp are simply the (root of the) product of the individual atomic parameters, whereas separate parameters - with no relation to the atomic ones - are defined in the original GROMOS force field. Hi Roman, I think there actually is a relation of the pair parameters to the individual atomic parameters in G43a1 as well as in G45a3 since all of the values are based on the same epsilon and sigma numbers. (For DMSO: epsilon = 1.297 kJ/mol for S, 1.7154 for O, 0.9414 for CH3 sigma = 0.356 nm for S, 0.263 for O, 0.366 for CH3) The difference in the C6/C12 pair parameters apparently is due to the use of different combination rules (see GROMACSmanual-4.0.pdf, chapter 5.3.3). For G45a3 equations (5.1) and (5.3) are used to calculate the respective pair parameters, whereas for G43a1 eq. (5.4) and after that (5.1) are used. So I guess the question is, which is the right way for the combination? Cheers, Markus The errors are there in the force field files distributed with gromacs version 4.0.5 all the way down to at least version 3.2.1 (it's as far as I've looked), and also in the ffG45a3.tar.gz file to be found at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields For example: The lines in ffG45a3nb.itp read: CDMSOSDMSO 1 0.009777435 2.1627421e-05 ... ODMSOSDMSO 1 0.004897196 4.0192831e-06 ODMSOCDMSO 1 0.0045335636 4.0434685e-06 However, they should be CDMSOSDMSO 1 0.0097827 2.16523e-05 ... ODMSOSDMSO 1 0.0052442 4.6094e-06 ODMSOCDMSO 1 0.0049187 4.7597e-06 as they are in the GROMOS 43a1 force field. A similar problem holds for chloroform (atoms CCHL, CLCHL and HCHL). Find attached a corrected version of ffG45a3nb.itp. Cheers, Roman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_energy= Different Average values?
Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. Energy Average RMSD Fluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034 259.015 -0.02151 -10.7574 Total Energy -215421 275.52 274.683 -0.14862 -74.3106 Temperature 302.825 1.51136 1.51125 -0.00013 -0.06277 Pressure (bar) 0.963727 133.498 133.335 0.045602 22.8012 Volume 221.643 0.362625 0.362424 8.36E-05 0.041823 Density (SI) 990.272 1.62111 1.6202 -0.00038 -0.18852 but the average values are different than calculation from the instantaneous data in the abc.xvg I sum up all the instantaneous data in the abc.xvg and average them. I got different average data as those shown up on the screen after g_energy command. What's wrong here? Thank you Lin ___ 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] .mdp = Dihedral Angles conflict Bond Constraints ?
Hi In the .mdp file, i set lincs-warnangle = 30. Will the dihedral angles be affected? Will the maximum, possible values of the dihedral angles be reduced because of the setup of the bond constraints? Thank you Lin ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] .mdp = Dihedral Angles conflict Bond Constraints ?
No. On Jul 6, 2009, at 20:58, Chih-Ying Lin chihying2...@gmail.com wrote: Hi In the .mdp file, i set lincs-warnangle = 30. Will the dihedral angles be affected? Will the maximum, possible values of the dihedral angles be reduced because of the setup of the bond constraints? Thank you Lin ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm= Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] including K ion in gromos96
hi, I am using gromacs 3.3.1 and ions.itp does not have K ion (in gromos96). I tried to include it by making K.itp and including in topology file. I get the following error.. Invalid order for directive atoms, file K.itp, line 1 I am not sure where I am wrong,,, thanks sadhna ___ 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] Segmentation Fault (Address not mapped)
Hi Mark, I added the energy group exclusions as indicated in your previous response but am still experiencing the same problem. I looked at the .log files and see that in one log file it tells me that my box is exploding. However, I do not have many molecules in my simulation and therefore do not think that it is possible that my box is exploding from pressure. Maybe if I re-state my simulation it will help you in providing me direction on what might be causing the problem. My simulation consists of a graphene lattice with a layer of ammonia molecules above it. The box is very large and there is lots of empty space in the box. So I am a little confused as to how the box could be exploding. Thanks again in advance for your help. Darrell Koskinen Date: Fri, 03 Jul 2009 11:41:45 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a4d61d9.6080...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lattice, and three times the height between the graphene lattice and the ammonia molecules. I am including the mdp file and the error message. Probably your system is exploding when integration fails with excessive forces. You should look at the bottom of stdout, stderr, *and* the .log file to diagnose. The error message you give below is merely the diagnostic trace from the MPI library, and it not useful for finding out what GROMACS thinks the problem might be. Further advice below. *** .mdp file title =FWS ;warnings =10 cpp =cpp ;define =-DPOSRES ;constraints=all-bonds integrator =md dt =0.002 ; ps nsteps =10 nstcomm =1000 nstxout =1000 ;nstvout=1000 nstfout =0 nstlog =1000 nstenergy =1000 nstlist =1000 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section added in to freeze hydrogen atoms at edge of graphene lattice to prevent movement of lattice ;energygrp_excl = Edge Edge Edge Grph Grph Grph freezegrps = Edge Grph ; Hydrogen atoms in graphene lattice are associated with the residue Edge See comments in 7.3.24 of manual. You need the energy group exclusions. Mark freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in all directions ;Tcoupl =berendsen ;tau_t =0.10.1 ;tc-grps=protein non-protein ;ref_t = 300 300 ;Pcoupl = parrinello-rahman ;tau_p = 0.5 ;compressibility = 4.5e-5 ;ref_p = 1.0 ;gen_vel = yes ;gen_temp = 300.0 ;gen_seed = 173529 *** *** ERROR IN OUTPUT FILE [node16:25758] *** Process received signal *** [node16:25758] Signal: Segmentation fault (11) [node16:25758] Signal code: Address not mapped (1) [node16:25758] Failing at address: 0xfffe1233e230 [node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80] [node16:25758] [ 1] /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6) [0x2ba295dd0606] [node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808) [0x2ba295dd4058] [node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de) [0x2ba295dba5be] [node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef) [0x2ba295ddeaff] [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193] [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0] [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9] [node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3833e1d8b4] [node16:25758] [ 9] mdrun_mpi [0x40429a] [node16:25758] *** End of error message *** mpirun noticed that job rank 7 with PID 25758 on node node16 exited on signal 11 (Segmentation fault). 7 processes killed (possibly by Open MPI) *** Could you please let me know what you think may be causing the fault? Much thanks in advance. Darrell Koskinen ___ 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
Re: [gmx-users] including K ion in gromos96
1. Update to gromacs 4.0.5 2. Your file K.Itp contains repeated instructions that it should not and therefore the error message. Build one new from the ions.itp. I am surprised gromos dos not have K+ ion! On Jul 6, 2009, at 23:52, sadhna joshi sadhna.jo...@gmail.com wrote: hi, I am using gromacs 3.3.1 and ions.itp does not have K ion (in gromos96). I tried to include it by making K.itp and including in topology file. I get the following error.. Invalid order for directive atoms, file K.itp, line 1 I am not sure where I am wrong,,, thanks sadhna ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] .mdp = Dihedral Angles conflict Bond Constraints ?
Subject: Re: [gmx-users] .mdp = Dihedral Angles conflict Bond Constraints ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ba75cb5-06ba-4766-b29d-6eeb086c0...@rug.nl Content-Type: text/plain; charset=us-ascii No. Hi: Why Not? lincs-warnangle = 30 this allows each covalent bond to rotate at most 30 degrees all bonds have less degree of freedom to rotate.. So, I think the dihedral angle will be affect... and the dihedral angle will some or less decreased. ?? Thank you Lin On Jul 6, 2009, at 20:58, Chih-Ying Lin chihying2...@gmail.com wrote: Hi In the .mdp file, i set lincs-warnangle = 30. Will the dihedral angles be affected? Will the maximum, possible values of the dihedral angles be reduced because of the setup of the bond constraints? Thank you Lin ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter= 1 lincs-warnangle = 30 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Segmentation Fault (Address not mapped)
darre...@ece.ubc.ca wrote: Hi Mark, I added the energy group exclusions as indicated in your previous response but am still experiencing the same problem. I looked at the .log files and see that in one log file it tells me that my box is exploding. However, I do not have many molecules in my simulation and therefore do not think that it is possible that my box is exploding from pressure. Sure, but if there's something malformed with your model physics or starting configuration, then large forces can make anything explode. Look at your structures at each point and see where things start to go wrong. Make sure you've used editconf on your starting structure to provide the right box dimensions. Mark Maybe if I re-state my simulation it will help you in providing me direction on what might be causing the problem. My simulation consists of a graphene lattice with a layer of ammonia molecules above it. The box is very large and there is lots of empty space in the box. So I am a little confused as to how the box could be exploding. Thanks again in advance for your help. Darrell Koskinen Date: Fri, 03 Jul 2009 11:41:45 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a4d61d9.6080...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lattice, and three times the height between the graphene lattice and the ammonia molecules. I am including the mdp file and the error message. Probably your system is exploding when integration fails with excessive forces. You should look at the bottom of stdout, stderr, *and* the .log file to diagnose. The error message you give below is merely the diagnostic trace from the MPI library, and it not useful for finding out what GROMACS thinks the problem might be. Further advice below. *** .mdp file title =FWS ;warnings =10 cpp =cpp ;define =-DPOSRES ;constraints=all-bonds integrator =md dt =0.002 ; ps nsteps =10 nstcomm =1000 nstxout =1000 ;nstvout=1000 nstfout =0 nstlog =1000 nstenergy =1000 nstlist =1000 ns_type =grid rlist =2.0 coulombtype =PME rcoulomb=2.0 vdwtype =cut-off rvdw=5.0 fourierspacing =0.12 fourier_nx =0 fourier_ny =0 fourier_nz =0 pme_order =4 ewald_rtol =1e-5 optimize_fft=yes ; This section added in to freeze hydrogen atoms at edge of graphene lattice to prevent movement of lattice ;energygrp_excl = Edge Edge Edge Grph Grph Grph freezegrps = Edge Grph ; Hydrogen atoms in graphene lattice are associated with the residue Edge See comments in 7.3.24 of manual. You need the energy group exclusions. Mark freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in all directions ;Tcoupl =berendsen ;tau_t =0.10.1 ;tc-grps=protein non-protein ;ref_t = 300 300 ;Pcoupl = parrinello-rahman ;tau_p = 0.5 ;compressibility = 4.5e-5 ;ref_p = 1.0 ;gen_vel = yes ;gen_temp = 300.0 ;gen_seed = 173529 *** *** ERROR IN OUTPUT FILE [node16:25758] *** Process received signal *** [node16:25758] Signal: Segmentation fault (11) [node16:25758] Signal code: Address not mapped (1) [node16:25758] Failing at address: 0xfffe1233e230 [node16:25758] [ 0] /lib64/libpthread.so.0 [0x3834a0de80] [node16:25758] [ 1] /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6) [0x2ba295dd0606] [node16:25758] [ 2] /usr/lib64/libmd_mpi.so.4(do_pme+0x808) [0x2ba295dd4058] [node16:25758] [ 3] /usr/lib64/libmd_mpi.so.4(force+0x8de) [0x2ba295dba5be] [node16:25758] [ 4] /usr/lib64/libmd_mpi.so.4(do_force+0x5ef) [0x2ba295ddeaff] [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193] [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) [0x4142f0] [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9] [node16:25758] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3833e1d8b4] [node16:25758] [ 9] mdrun_mpi [0x40429a] [node16:25758] *** End of error message *** mpirun noticed that job rank 7 with PID 25758 on node node16 exited on signal 11 (Segmentation fault). 7 processes killed (possibly by Open MPI) *** Could you please let me know what you think may be causing the fault? Much thanks in advance. Darrell Koskinen
Re: [gmx-users] Shift electrostatic summation
Shuangxing Dai wrote: Dear all, I was trying to modify the Shift option of electrostatic summation. Mainly I want to modify the formulas of this electrostatic summation. From the manual page 69, the modified non-bonded interactions, the formulas about Shift is there. In the file /src/gmxlib/shift_util.c, there are these formulas. So is this the only file for Shift? Since I have added some printf lines to this file, I do not see the result when I recompile and use Shift. I doubt whether this function was called to do Shift. Or is there any other file related with the Shift method and I need to change? It won't be called... the routines in src/gmxlib/nonbonded/xxx are used. The easiest way to experiment with changes to (nonbonded) interactions is to use table potentials. See various sections of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_energy= Different Average values?
Chih-Ying Lin wrote: Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. Energy Average RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711-63.5543 Kinetic En. 51901.5 259.034 259.015 -0.02151-10.7574 Total Energy -215421 275.52 274.683 -0.14862-74.3106 Temperature 302.825 1.51136 1.51125 -0.00013 -0.06277 Pressure(bar) 0.963727133.498 133.335 0.04560222.8012 Volume 221.643 0.3626250.3624248.36E-050.041823 Density (SI)990.272 1.62111 1.6202 -0.00038 -0.18852 but the average values are different than calculation from the instantaneous data in the abc.xvg I sum up all the instantaneous data in the abc.xvg and average them. I got different average data as those shown up on the screen after g_energy command. The average values reported in the .edr file are not necessarily the averages of the values in the .edr file. See manual appendix. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Competition of electric force and hydrophobicity
Hi Is there any idea about the competition of electric force and hydrophobicity ? thank you Lin ___ 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] using editconf to duplicate membrane
Dear all, I want to extend the membrane into 512 POPC with the starting structure of 128 POPC. I 've used :- editconf -f xxx.pdb -scale 2 2 1 -o zzz.pdb. I noticed that the pdb file that generated by editconf have only 1 set of 128 popc. Using vmd, the extended structure is in pieces, the no bond between each atom. When i checked the pdb file, i didn't find any atomic coordination for the extended set of POPC. Did i missed out anything here? or what I've done is wrong here? When i used genconf , the extended structure looks fine. But, i found some discussion regarding genconf whereby the structure will not be in one pieces if this command is used. Please advice. Thank in advance. Regards, bing ___ 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
