[gmx-users]Simulated annealing
Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title= Water annealing simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps dt = 0.001; 1fs nsteps = 10 ; 1ps ; For exact run continuation or redoing part of a run init_step = 0 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 ; 10ps nstvout = 1 ; 10ps nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 ; Output frequency for energies to log file and energy file nstlog = 0 nstenergy= 1000 ; 1ps ; Output frequency and precision for xtc file ;nstxtcout= 0 ;xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; check for the range 0.1 to 0.15 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling ;Tcoupl = berendsen ; Groups to couple separately ;tc-grps = system ; Time constant (ps) and reference temperature (K) ;tau-t = 0.1 ;ref-t= 360 ; simulated anealing annealing= single annealing_npoints= 2 annealing_time = 0 0 annealing_temp = 360 0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen-temp = 360 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no --- Problem: Having done the simulations, the output shows ( ener.edr , Temperature) a high temperature value around 850K. Clearly I did something wrong in my parameter file. --- the temperature extracted after the simulations --- s0 legend Temperature 0.00 376.058044 1.00 864.033020 2.00 873.607605 3.00 851.308838 4.00 847.223877 5.00 860.511841 6.00 813.547241 7.00 845.261658 8.00 872.090027 9.00 852.079468 10.00 849.152466 11.01 850.055237 12.01 834.468323 13.01 861.107300 14.01 828.380493 15.01 850.166809 16.00 850.382019 17.00 847.214478 18.00 851.201538 19.00 857.533691 20.00 849.760071 21.02 864.907715 22.02 837.307495 23.02 827.407593 24.02 841.464111 25.02 863.330688 26.02 841.096069 27.02 856.469910 28.02 854.449768 29.02 845.534973 30.02 853.421448 31.02 825.198059 32.00 857.317566 33.00 823.510925 34.00 858.875122 35.00 880.710266 36.00 853.692749 37.00 847.079468 38.00 851.004822 39.00 858.75 40.00 872.787048 41.04 843.033813 42.04 874.984009 43.04 845.272583 44.04 822.993713 45.04 863.116455 46.04 865.640198 47.04 873.489563 48.04 849.170776 49.04 861.631958 50.04
Re: [gmx-users]Simulated annealing
JMandumpal wrote: Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title= Water annealing simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps dt = 0.001; 1fs nsteps = 10 ; 1ps ; For exact run continuation or redoing part of a run init_step = 0 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 ; 10ps nstvout = 1 ; 10ps nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 ; Output frequency for energies to log file and energy file nstlog = 0 nstenergy= 1000 ; 1ps ; Output frequency and precision for xtc file ;nstxtcout= 0 ;xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; check for the range 0.1 to 0.15 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling ;Tcoupl = berendsen ; Groups to couple separately ;tc-grps = system ; Time constant (ps) and reference temperature (K) ;tau-t = 0.1 ;ref-t= 360 ; simulated anealing annealing= single annealing_npoints= 2 annealing_time = 0 0 ^^^ I think this should be annealing_time = 0 100 in your case, right? Jochen annealing_temp = 360 0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen-temp = 360 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no --- Problem: Having done the simulations, the output shows ( ener.edr , Temperature) a high temperature value around 850K. Clearly I did something wrong in my parameter file. --- the temperature extracted after the simulations --- s0 legend Temperature 0.00 376.058044 1.00 864.033020 2.00 873.607605 3.00 851.308838 4.00 847.223877 5.00 860.511841 6.00 813.547241 7.00 845.261658 8.00 872.090027 9.00 852.079468 10.00 849.152466 11.01 850.055237 12.01 834.468323 13.01 861.107300 14.01 828.380493 15.01 850.166809 16.00 850.382019 17.00 847.214478 18.00 851.201538 19.00 857.533691 20.00 849.760071 21.02 864.907715 22.02 837.307495 23.02 827.407593 24.02 841.464111 25.02 863.330688 26.02 841.096069 27.02 856.469910 28.02 854.449768 29.02 845.534973 30.02 853.421448 31.02 825.198059 32.00 857.317566 33.00 823.510925 34.00 858.875122 35.00 880.710266 36.00 853.692749 37.00 847.079468 38.00 851.004822 39.00
Re: [gmx-users]Simulated annealing
On 27 Oct 2008 06:36:09 - JMandumpal [EMAIL PROTECTED] wrote: Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title= Water annealing simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps dt = 0.001; 1fs nsteps = 10 ; 1ps ; For exact run continuation or redoing part of a run init_step = 0 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 ; 10ps nstvout = 1 ; 10ps nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 ; Output frequency for energies to log file and energy file nstlog = 0 nstenergy= 1000 ; 1ps ; Output frequency and precision for xtc file ;nstxtcout= 0 ;xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; check for the range 0.1 to 0.15 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; OPTIONS FOR WEAK COUPLING ALGORITHMS in what follows you have commented out the temperature coupling details. I have never used SA but this for sure will not help the program controling the temperature! Put these back on should help! :)) ; Temperature coupling ;Tcoupl = berendsen ; Groups to couple separately ;tc-grps = system ; Time constant (ps) and reference temperature (K) ;tau-t = 0.1 ;ref-t= 360 ; simulated anealing annealing= single annealing_npoints= 2 annealing_time = 0 0 annealing_temp = 360 0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen-temp = 360 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no --- Problem: Having done the simulations, the output shows ( ener.edr , Temperature) a high temperature value around 850K. Clearly I did something wrong in my parameter file. --- the temperature extracted after the simulations --- s0 legend Temperature 0.00 376.058044 1.00 864.033020 2.00 873.607605 3.00 851.308838 4.00 847.223877 5.00 860.511841 6.00 813.547241 7.00 845.261658 8.00 872.090027 9.00 852.079468 10.00 849.152466 11.01 850.055237 12.01 834.468323 13.01 861.107300 14.01 828.380493 15.01 850.166809 16.00 850.382019 17.00 847.214478 18.00 851.201538 19.00 857.533691 20.00 849.760071 21.02 864.907715 22.02 837.307495 23.02 827.407593 24.02 841.464111 25.02 863.330688 26.02 841.096069 27.02 856.469910 28.02 854.449768 29.02 845.534973 30.02 853.421448 31.02 825.198059 32.00 857.317566 33.00 823.510925 34.00 858.875122 35.00 880.710266 36.00 853.692749 37.00 847.079468 38.00 851.004822 39.00 858.75 40.00 872.787048
Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server
Am Sonntag, 26. Oktober 2008 schrieb Lee Soin: Everything works fine by setting NOASSEMBLYLOOPS. Thanks! 2008/10/26 Mark Abraham [EMAIL PROTECTED] Lee Soin wrote: Single CPU run. These are the last lines of the log file: Configuring nonbonded kernels... Testing ia64 CPU family...Unknown Itanium You might want to test the speed without assembly kernels by setting the NOASSEMBLYLOOPS environment variable. Try that... My guess is that the ia64 kernel isn't working on your machine, for some unknown reason. Well, I assume that it runs on an Itanium Montecito cores - here we have the same issue. AFAIR there was a discussion in February on the list that this will not be fixed so soon. Anyways - intel fortran compilers on itanium probably will give you a pretty good performance compared to assembly nb-kernels. Best Martin ___ 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] table_bonded.xvg
Hi, When I type : mdrun -tableb bond_b0.xvg -v I get following message: Program mdrun, VERSION 4.0 Source code file: futil.c, line: 527 Fatal error: Library file bond_b0_b0.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) --- Thats what confused me when I type mdrun -tableb It reads table_b0.xvg Greetings Andrzej Hi, According to me it does not. I never change the default names. But with the default names the table file name option is table.xvg and for a tabulated bond table number 0, it correctly opens table_b0.xvg Berk From: A.Rzepiela at rug.nl To: gmx-users at gromacs.org Date: Fri, 24 Oct 2008 13:45:53 +0200 Subject: [gmx-users] table_bonded.xvg Dear Users In gromacs 4.0, in file force.c in function make_bonded_tables line (1007) sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,_%s%d.%s, tabext, i, ftp2ext(efXVG)); produces table_bonded_bonded.xvg instead of table_bonded.xvg Greetings Andrzej Rzepiela ___ gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] splitting a trajectory according to atoms using trjconv
Hi, I read GROMACS bugzilla report of bug 107 (http://bugzilla.gromacs.org/show_bug.cgi?id=107)[1] and have to admit that I have no experience using trjconv. I really just need a push in the right direction -- I can't seem to find any decent explanation on how to use trjconv for this purpose anywhere on the net. What I'm trying to do is take a trajectory file I generated, and perform a trajectory analysis of two specific atoms in the molecule. Since g_traj only takes one index group, this is a problem. In particular, I want to automate the process and use non-interactive command-line calls. I think I should split the entire-molecule's-trajectory so that I have a separate trajectory file for each atom I would like to look at, and then serially run g_traj for each atom-trajectory. How do I use trjconv to split one trajectory file into a few, according to index groups or atoms? -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. Links: -- [1] http://bugzilla.gromacs.org/show_bug.cgi?id=107) ___ 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] splitting a trajectory according to atoms using trjconv
Inon Sharony wrote: Hi, I read GROMACS bugzilla report of bug 107 (http://bugzilla.gromacs.org/show_bug.cgi?id=107)[1] and have to admit that I have no experience using trjconv. I really just need a push in the right direction -- I can't seem to find any decent explanation on how to use trjconv for this purpose anywhere on the net. What I'm trying to do is take a trajectory file I generated, and perform a trajectory analysis of two specific atoms in the molecule. Since g_traj only takes one index group, this is a problem. In particular, I want to automate the process and use non-interactive command-line calls. Have a look at this: http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive I think I should split the entire-molecule's-trajectory so that I have a separate trajectory file for each atom I would like to look at, and then serially run g_traj for each atom-trajectory. How do I use trjconv to split one trajectory file into a few, according to index groups or atoms? Just make the index groups you wish, and pass them to trjconv with -n. -Justin -- Inon Sharony ינון שרוני +972(3)6407634 atto.TAU.ac.IL/~inonshar Please consider your environmental responsibility before printing this e-mail. Links: -- [1] http://bugzilla.gromacs.org/show_bug.cgi?id=107) ___ 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 thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Adding Na ions to DPPG
Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdrun doesn't run in version 4.0 on sgi server
Carsten Kutzner wrote: Hi, Mark Abraham wrote: Lee Soin wrote: By invoking uname -a: Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux I don't know any other command to retrieve system information. Hmm, that looks like an SGI Altix 4700. IA64 kernels work on those machines. Well, not exactly. Ah, oops. I was thinking of the Altix 3700 series, which predates Montecito. My bad. They work in combination with Gromacs version = 3.3.x, but at least I have never managed to get them working with this year's CVS Gromacs or Gromacs 4.x - see also http://www.gromacs.org/pipermail/gmx-developers/2008-February/002405.html The strange thing is that these inner loops have not changed since 3.3.x, so the problem might be somewhere else. But actually the Fortran loops have a quite decent performance on that machine compared to assembly: In a single-CPU test I did with gmx 3.3 they were just about 10% slower. Good to know. Lee should definitely compare performance when using configure with and without --enable-fortran (and using --disable-cpu-optimization to avoid needing to set the environment variable). Mark ___ 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] Adding Na ions to DPPG
Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. That doesn't make sense to me. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Sodium is not going to form any bond. It's a labile ion, so needs its own [ molecule ] section. The easiest approach is to construct a topology for the anion, and then use genion to add suitable amounts of Na+ afterwards. Check out some tutorial material for the approach here. Mark ___ 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] Adding Na ions to DPPG
Use the Gromacs program genion for that purpose. This replaces water molecules by the ions you specify. You may need to change the topology afterwards manually. Make sure, you put an #include ions.ipt near the top of the .top-file, this contains the force field parameters for ions. Best wishes Andreas -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peyman Yamin Sent: 27 October 2008 12:36 To: gmx-users Subject: [gmx-users] Adding Na ions to DPPG Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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] Adding Na ions to DPPG
Thanks a lot for the replies, I replace the O in DPPG because I thought it's practical to get the topology of the quasi-DPPG (which has no charge cause the O is connected to the P) from prodrg, and then delete the O and replace it with Na and delete the bond of P with it and try to tell gromacs it's just a non-bonded Na around the P! since it's always around the P replacing the O which was bond to P made sense to me from the coordinates (distance to P, etc.) point of view. Am I doing strange things?? I'm not sure if I have to use genion since my zwitterionic DPPG has always its Na+ beside its O-. On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. I thought since O on P is gone it will be -1 charged, so a +1 Na will balance it, won't it?? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. Well I do include it. So shouldn't I worry about the nonbonding params and stuff? like those in topology file? Actually an existential question for me always is that if everything goes OK by adding the FF itp, then why does prodrg give me all the params for bonds, dihedrals, angles and etc.?? So, genion or manually replace? and how please...I mean, I don't want to pass my task to others, but well, a bit of more detailed help would enlight me a great deal ;) Cheers, Peyman APPENDIX! * This is the top for the DPPG with the unwanted O --- say O number 24. ** The question is if I simply change that to Na (of course in pdb as well) what changes should I make in other switches? I see non of non-bonding context! (pairs?) [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 DRG CBL 1 -0.019 15.0350 2 CH2 1 DRG CBK 10.006 14.0270 3 CH2 1 DRG CBJ 10.006 14.0270 4 CH2 1 DRG CBI 10.007 14.0270 5 CH2 1 DRG CBH 20.000 14.0270 6 CH2 1 DRG CBG 30.000 14.0270 7 CH2 1 DRG CBF 40.000 14.0270 8 CH2 1 DRG CBE 50.000 14.0270 9 CH2 1 DRG CBD 60.000 14.0270 10 CH2 1 DRG CBC 70.000 14.0270 11 CH2 1 DRG CBB 80.000 14.0270 12 CH2 1 DRG CBA 90.000 14.0270 13 CH2 1 DRG CAZ100.039 14.0270 14 CH2 1 DRG CAY100.039 14.0270 15 CH2 1 DRG CAX100.039 14.0270 16 C 1 DRG CAV100.232 12.0110 17 O 1 DRG OAW10 -0.377 15.9994 18OA 1 DRG OAU10 -0.108 15.9994 19 CH1 1 DRG CAT100.136 13.0190 20 CH2 1 DRG CBM110.054 14.0270 21OA 1 DRG OBN11 -0.094 15.9994 22 P 1 DRG PBO110.954 30.9738 23OA 1 DRG OBP11 -0.410 15.9994 24OA 1 DRG OBQ11 -0.410 15.9994 25OA 1 DRG OBR11 -0.094 15.9994 26 CH2 1 DRG CBS120.034 14.0270 27 CH1 1 DRG CBT120.070 13.0190 28OA 1 DRG OBW12 -0.117 15.9994 29 H 1 DRG HCQ120.013 1.0080 30 CH2 1 DRG CBU130.069 14.0270 31OA 1 DRG OBV13 -0.086 15.9994 32
Re: [gmx-users] Adding Na ions to DPPG
On Monday 27 October 2008 14:08, Mark Abraham wrote: Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. That doesn't make sense to me. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Sodium is not going to form any bond. It's a labile ion, so needs its own [ molecule ] section. The easiest approach is to construct a topology for the anion, and then use genion to add suitable amounts of Na+ afterwards. Check out some tutorial material for the approach here. Right, but can't I have them all included in a single top?? What shall I put into the topology of the cation then? I have a single DPPG molecule in water/octanol. So I thought I might just embed the Na inside the DPPG top. in the end DPPG HAS a Na actually, though non-bonded! If I'm way away from making sense then would be happy to know the logical way. about genion I thought it's mainly for adding the ions to the solvent, but I should have exactly one Na. Be well, Peyman Mark ___ 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 -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] HYP GROMOS
Hello, Thank you for your response. The topology file was propared using pdb2gmx. I changed one of the improper dihedral angles (CG-CD-CB-O) for HYP to (CG-CD-O-CB) and CG of HYP stopped inverting. There seems to be much less of proper dihedrals in the topology file on using pdb2gmx for GROMOS force fields compared to OPLS-AA or AMBER. For example, for the OPLS-AA there are 3 dihedrals in the topology around the N-CA bond: C(i-1) - N - Ca - Ha C(i-1) - N - Ca - C C(i-1) - N - Ca - Cb Following the same logic, there should be two dihedrals in the GROMOS topology file, but there is only one (C(i-1) - N - Ca - C). Any special reason for this? Abil Date: Sun, 19 Oct 2008 10:52:13 +0200 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] HYP GROMOS Abil Aliev wrote: Hello, I have done calculations using standard GROMOS 43a1 and 53a6 parameters (GROMACS 3.3.3) for a 4-hydroxy-L-proline derivative (HYP), where the gamma-OH and the alpha-CO groups are trans to each other in the starting structure. However, over the course of MD the trans-configuration of these two substituents changes into a cis-configuration, which was not supposed to happen. Is there any way to avoid such isomerisation? Dihedral potentials, maybe you need to add an improper... Abil Get the best wallpapers on the Web - FREE. Click here! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Catch up on all the latest celebrity gossip http://clk.atdmt.com/GBL/go/115454061/direct/01/___ 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] Adding Na ions to DPPG
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPGx NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: On Monday 27 October 2008 14:08, Mark Abraham wrote: Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. That doesn't make sense to me. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Sodium is not going to form any bond. It's a labile ion, so needs its own [ molecule ] section. The easiest approach is to construct a topology for the anion, and then use genion to add suitable amounts of Na+ afterwards. Check out some tutorial material for the approach here. Right, but can't I have them all included in a single top?? What shall I put into the topology of the cation then? I have a single DPPG molecule in water/octanol. So I thought I might just embed the Na inside the DPPG top. in the end DPPG HAS a Na actually, though non-bonded! Alright, now I understand. So you will have several different topologies to deal with. You don't need to merge DPPG/Na+ into one! You have separate topologies for water and octanol, too, don't you? You could use the topology from PRODRG as dppg.itp, for example, and construct a .top that has the following: #include ffG43a1.itp #include dppg.itp #include spc.itp #include octanol.itp #include ions.itp [ molecules ] DPPGx SOL y OCT z NA+ 1 All bonded and non-bonded parameters will then be read from the appropriate force field files, without merging anything! -Justin If I'm way away from making sense then would be happy to know the logical way. about genion I thought it's mainly for adding the ions to the solvent, but I should have exactly one Na. Be well, Peyman Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPG x NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. Well this looks great! I simulate one single DPPG in solvent. and you know, this Na+ is not in solvent but a part of DPPG. So you mean I just make a DPPG with an O which has no H so is minus and then use genion to add Na? will it place the Na aroung O hopefully? I think if I put no H arounf O the prodrg will force me to have it! so I should delete it and replace it with Na? or I should never use the word replace at all??? Thanks again ;) Peyman -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Adding Na ions to DPPG
Peyman Yamin wrote: On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: Peyman Yamin wrote: On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: Actually I'm doing a funny mistake telling I should replace an O with an Na! (probably because of high adrenaline level in my blood for the deadline is near!) I should just put one Na beside the O I have! I simply have a PO4 where one O has no H and thus is negative. an Na+ should accompany this O. Well that makes more sense. I'm assuming you have a DPPG bilayer with solvent? Or are you simulating a single DPPG in vacuo? If it's a bilayer in solution, just use genion; you can even specify exactly how many Na+ you want using -np. If the topology organization is confusing you, refer to Chapter 5 of the manual. If you make a .top for DPPG, you can specify: [ molecules ] DPPGx NA+ 1 (or whatever) after including the appropriate force field call and ions.itp; the parameters for all atom types are taken from these files. Well this looks great! I simulate one single DPPG in solvent. and you know, this Na+ is not in solvent but a part of DPPG. So you mean I just make a DPPG with an O which has no H so is minus and then use genion to add Na? will it place the Na aroung O hopefully? I think if I put no H arounf O the prodrg will force me to have it! so I should delete it and replace it with Na? or I should never use the word replace at all??? Well, the Na+ may be associated with DPPG electrostatically, but they are still distinct chemical entities. You can have a DPPG that has a net -1 charge; certainly all chemical species are not net neutral! Indeed, genion will place Na+ in whatever solvent you choose, but may not necessarily be bound to DPPG. Some simulation may show the association, however. And no, don't replace any part of your DPPG. Because then you don't really have DPPG any more do you? -Justin Thanks again ;) Peyman -Justin Peyman Yamin wrote: Dear GMX users, I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure with the Na replaced with O. I get a .top with this from prodrg and try to add the Na manually at the right place by removing the corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem: Are you trying to replace the O in DPPG with Na+? Or are you simply trying to add ions to the surrounding solvent (water)? If you just need ions in the solvent, use genion; you don't have to do it manually. * In .top file, as far as I can understand, I should just replace OA with NA+ and set the mass and charge. DPPG has a centre: [ O-P(O)=O ] - The Na+ should be around this with +1 charge. should I put charge +1 ? Again, I'm not clear on what you're trying to accomplish. If you replace one of these oxygen atoms, you will likely not have an integer charge within the DPPG molecule itself. * which parameters should I place in the top as the Na+ is not bonding. I need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA) but I'm not sure where should I put it in the top file. What should I insert manually in top file at all? Simply #include ffG43a1.itp at the top of your .top file; it will include nonbonded and bonded parameters for all the atoms in the system. -Justin Thanks in advance for the time, I've been away for some time from GMX and might sound Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] trjcat
Dear users, I have nearly 2000 xtc files to concatenate. If I type them all at the command prompt (or by using a small script) they are stiched well. But, If I stich the first 1000 and the next 1000 separately and then if I try to stich these two together I could not stich them properlty. Is there any way to stich the group of xtc files together? Ram. ___ 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] trjcat
rams rams wrote: Dear users, I have nearly 2000 xtc files to concatenate. If I type them all at the command prompt (or by using a small script) they are stiched well. But, If I stich the first 1000 and the next 1000 separately and then if I try to stich these two together I could not stich them properlty. Is there any way to stich the group of xtc files together? Can you show the actual command lines you're using to do this? -Justin Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Dihedral not counted?
Hi all, I defined my residues for Polystyrene (first, last and inner monomers), with the coresponding bonds, angles, dihedrals and impropers, including also the conectivities (as + and - atoms of the next or previous residue). Pdb2gmx runs without error or warning, but it counts less dihedrals then I would expect. I did run the same for dimer and trimer. For dimer is ok, for trimer starts to count 1 dihedral less, and for the chain with 80 monomers corespondingly 78 dihedrals less, which means that the error should be in the inner residue. I checked many times, but the dihedral which is missing in the .top file is defined in the .rtp. So I have really no clue what is wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me. Please give me a good idea :o) Thanks in advance. Andrea ___ 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] Dihedral not counted?
Andrea Muntean wrote: Hi all, I defined my residues for Polystyrene (first, last and inner monomers), with the coresponding bonds, angles, dihedrals and impropers, including also the conectivities (as + and - atoms of the next or previous residue). Pdb2gmx runs without error or warning, but it counts less dihedrals then I would expect. I did run the same for dimer and trimer. For dimer is ok, for trimer starts to count 1 dihedral less, and for the chain with 80 monomers corespondingly 78 dihedrals less, which means that the error should be in the inner residue. I checked many times, but the dihedral which is missing in the .top file is defined in the .rtp. So I have really no clue what is wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me. Please give me a good idea :o) Without seeing the .rtp entry and the relevant portion of the resulting .top, it's hard to say. Can you post those pieces of information? -Justin Thanks in advance. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Hi Justin, here are the relevant parts, as pdf files. I miss a dihedral between the atoms 2, 9, 10 and 17, which corresponds to the -CH CH2 CH +CH2 dihedral in the PS residue in the RTP entry. For the trimer I should have 26 dihedrals, but in the TOP file I get only 25 (I mean only the proper dihedrals, the impropers are OK). Thanks for your help. Andrea RTP.pdf Description: Adobe PDF document TrimerTOP.pdf Description: Adobe PDF document ___ 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] Dihedral not counted?
Andrea Muntean wrote: Hi Justin, here are the relevant parts, as pdf files. I miss a dihedral between the atoms 2, 9, 10 and 17, which corresponds to the -CH CH2 CH +CH2 dihedral in the PS residue in the RTP entry. Please send them as plain text to the list so everyone can see them without having to download the files (and so they can be archived for reference). -Justin For the trimer I should have 26 dihedrals, but in the TOP file I get only 25 (I mean only the proper dihedrals, the impropers are OK). Thanks for your help. Andrea -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Well, there's no real problem, per se. Everything that you've given pdb2gmx is in the topology; the issue is that you haven't specified any parameters for those dihedrals: CH CB CG1 CG2 CH CB CG5 CG4 2 3 4 5 1 2 3 8 7 1 Makes sense that they'd be missing. If you're dealing with polystyrene, maybe consider basing the dihedrals off of those contained in the PHE sidechain in the Gromos force field you appear to be using. -Justin Andrea Muntean wrote: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] CH3 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle CH3 CH +CH2ga_12 CH3 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH3 gi_1 CH +CH2CH3 CB gi_1 CH CH3 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle -CH CH2 CH ga_12 CH2 CH +CH2ga_12 CH2 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH2 gi_1 CH +CH2CH2 CB gi_1 CH CH2 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 -CH CH2 CH CB gd_16 -CH CH2 CH +CH2gd_16 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [ PSN ] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 CH3 CH3 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH CH3 gb_26 [angles] -CH CH2 CH ga_12 CH2 CH CH3 ga_12 CH2 CH CB ga_12 CB CH CH3 ga_12 CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1
[gmx-users] Double vs. Charged Single bonded Oxygen in GROMOS96.1
Hi again dears, I should ask for another comment. I have a Phorphorus to which two Oxygen atoms are bonded. One O is double bonded and the other has only a single bond while being negatively charged. In the topology file I get from prodrg both Os are denoted with OA (GROMOS96.1) atom type. both have the same charge (-0.421) and mass (15.9994). I guess the charge is reasonable for the double-bonded one, but not for the one with a single bond and a free electron. How could I correct this? Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dihedral not counted?
Sorry, once again for everybody in the list: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] CH3 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle CH3 CH +CH2ga_12 CH3 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH3 gi_1 CH +CH2CH3 CB gi_1 CH CH3 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle -CH CH2 CH ga_12 CH2 CH +CH2ga_12 CH2 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH2 gi_1 CH +CH2CH2 CB gi_1 CH CH2 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 -CH CH2 CH CB gd_16 -CH CH2 CH +CH2gd_16 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [ PSN ] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 CH3 CH3 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH CH3 gb_26 [angles] -CH CH2 CH ga_12 CH2 CH CH3 ga_12 CH2 CH CB ga_12 CB CH CH3 ga_12 CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB CH3CH2 gi_1 CH CH3 CH2CB gi_1 CH CH2 CB CH3 gi_1 [dihedrals] ;in the chain - 3-fold (n=3) -CH CH2
Re: [gmx-users] trjcat
Dear Justin, The following is the command I am using: trjcat -ffirst.xtc second.xtc -o total.xtc first.xtc and second.xtc are the stiched xtc files of first 1000 and second 1000 xtc files. Ram. On Mon, Oct 27, 2008 at 11:10 AM, Justin A. Lemkul [EMAIL PROTECTED] wrote: rams rams wrote: Dear users, I have nearly 2000 xtc files to concatenate. If I type them all at the command prompt (or by using a small script) they are stiched well. But, If I stich the first 1000 and the next 1000 separately and then if I try to stich these two together I could not stich them properlty. Is there any way to stich the group of xtc files together? Can you show the actual command lines you're using to do this? -Justin Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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] Double vs. Charged Single bonded Oxygen in GROMOS96.1
Peyman Yamin wrote: Hi again dears, I should ask for another comment. I have a Phorphorus to which two Oxygen atoms are bonded. One O is double bonded and the other has only a single bond while being negatively charged. In the topology file I get from prodrg both Os are denoted with OA (GROMOS96.1) atom type. both have the same charge (-0.421) and mass (15.9994). I guess the charge is reasonable for the double-bonded one, but not for the one with a single bond and a free electron. How could I correct this? There is no true double or single bond. Think resonance! -Justin Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjcat
rams rams wrote: Dear Justin, The following is the command I am using: trjcat -ffirst.xtc second.xtc -o total.xtc first.xtc and second.xtc are the stiched xtc files of first 1000 and second 1000 xtc files. And so what happens that makes you think something is wrong? Are you getting an error message? -Justin Ram. On Mon, Oct 27, 2008 at 11:10 AM, Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: rams rams wrote: Dear users, I have nearly 2000 xtc files to concatenate. If I type them all at the command prompt (or by using a small script) they are stiched well. But, If I stich the first 1000 and the next 1000 separately and then if I try to stich these two together I could not stich them properlty. Is there any way to stich the group of xtc files together? Can you show the actual command lines you're using to do this? -Justin Ram. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] table command
Hi all users, I just use the command mdrun -table table_nonbond.xvg to run the table file but it always shows that Fatal error: Tables in file table_nonbond.xvg not long enough for cut-off: should be at least 1.90 nm Actually, I have listed all the values up to 2.000nm in the file so I get a little confused about this error; Can anyone of you give me some suggestions? Thank you in advance. Yang ___ 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] Double vs. Charged Single bonded Oxygen in GROMOS96.1
On Monday 27 October 2008 18:08, Justin A. Lemkul wrote: Peyman Yamin wrote: Hi again dears, I should ask for another comment. I have a Phorphorus to which two Oxygen atoms are bonded. One O is double bonded and the other has only a single bond while being negatively charged. In the topology file I get from prodrg both Os are denoted with OA (GROMOS96.1) atom type. both have the same charge (-0.421) and mass (15.9994). I guess the charge is reasonable for the double-bonded one, but not for the one with a single bond and a free electron. How could I correct this? There is no true double or single bond. Think resonance! Impressive answer! But, well, I'm not sure about that resonance thing? ...C-O-P(+3)-O-C... So far it's OK! but P still has 3 fellow electrons to share. it does share two of them at once with another O. I understand till here. there is another O who wants to get 2 electrons shared, but only receives one: it needs more = so we call it a negatively charges fellow oxygen, don't we? Well I'm well aware of my chemistry knowledge fading away, but you'll tell me an OA will do well for both?? Thanks for the time, indeed, Peyman -Justin Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file for methane.
xianghong qi wrote: Hello, Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field? Thanks in advance. For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5. -Justin -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double vs. Charged Single bonded Oxygen in GROMOS96.1
Peyman Yamin wrote: On Monday 27 October 2008 18:08, Justin A. Lemkul wrote: Peyman Yamin wrote: Hi again dears, I should ask for another comment. I have a Phorphorus to which two Oxygen atoms are bonded. One O is double bonded and the other has only a single bond while being negatively charged. In the topology file I get from prodrg both Os are denoted with OA (GROMOS96.1) atom type. both have the same charge (-0.421) and mass (15.9994). I guess the charge is reasonable for the double-bonded one, but not for the one with a single bond and a free electron. How could I correct this? There is no true double or single bond. Think resonance! Impressive answer! But, well, I'm not sure about that resonance thing? ...C-O-P(+3)-O-C... So far it's OK! but P still has 3 fellow electrons to share. it does share two of them at once with another O. I understand till here. there is another O who wants to get 2 electrons shared, but only receives one: it needs more = so we call it a negatively charges fellow oxygen, don't we? I think there are going to be two distinct atom types. For a few examples of how to deal with phosphates, see the .rtp entry for ATP, or look at the lipids that Peter Tieleman makes available online. If we consider a traditional Lewis structure for the phosphodiester (hopefully this translates alright): O || R--O--P--O--R | O- Really the =O and --O^- are equivalent in terms of atom type (OM in Gromos) and charge. The O in the phosphodiester linkages are likely to bear similar charges, but have a different atom type (OE in Gromos). Hence why proper parameterization takes a substantial amount of time. Be careful if you're using the topology straight from PRODRG. Its interpretation of charge groups and charges often requires a bit of refinement. Also realize that Gromos96 is not the best for reproducing the properties of a lipid, although I don't know if isolated lipids have been considered. The Berger lipid parameters (Gromos/OPLS combination) are widely used...but that's a whole other debate :) Well I'm well aware of my chemistry knowledge fading away, but you'll tell me an OA will do well for both?? Maybe for the phosphodiester O, but not for the =O and --O^-; they are more like a carbonyl O (atom type OM). -Justin Thanks for the time, indeed, Peyman -Justin Cheers, Peyman -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] H2O water density = 6.4617 g/l 1000 g/l
Hi I am creating the water box with the following command. The maxsol = 800; but # of SOL = 27; The H2O water density = 6.4617 g/l 1000 g/l Did I do anything wrong on my genbox command or 1w.gro file? Thank you Lin genbox -cp 1w.gro -cs 1w.gro -o box.gro -box 5 5 5 -maxsol 800 Output configuration contains 81 atoms in 27 residues Volume : 125 (nm^3) Density: 6.4617 (g/l) Number of SOL molecules: 27 Here is the 1w.gro 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 3 1SOL OW1.230.628.113 1SOLHW12.137.626.150 1SOLHW23.231.589.021 1.86206 1.86206 1.86206 ___ 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] Dihedral not counted?
Strange enough, those dihedrals are there, but the dihedral between atoms 2 9 10 and 17 is missing (in the main chain), altough defined in the PS residue (as -CH CH2 CH +CH2). I am still clueless... Greetings, Andrea 2008/10/27 Justin A. Lemkul [EMAIL PROTECTED]: Well, there's no real problem, per se. Everything that you've given pdb2gmx is in the topology; the issue is that you haven't specified any parameters for those dihedrals: CH CB CG1 CG2 CH CB CG5 CG4 2 3 4 5 1 2 3 8 7 1 Makes sense that they'd be missing. If you're dealing with polystyrene, maybe consider basing the dihedrals off of those contained in the PHE sidechain in the Gromos force field you appear to be using. -Justin Andrea Muntean wrote: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] CH3 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle CH3 CH +CH2ga_12 CH3 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH3 gi_1 CH +CH2CH3 CB gi_1 CH CH3 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold (n=3) CH3 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 ;around CH-CB - 2-fold (n=2) CH3 CH CB CG5 gd_1 CH3 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [PS] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH +CH2gb_26 [angles] ;109,5 angle -CH CH2 CH ga_12 CH2 CH +CH2ga_12 CH2 CH CB ga_12 CB CH +CH2ga_12 ;120 angle CH CB CG1 ga_26 CH CB CG5 ga_26 CG1 CB CG5 ga_26 CB CG1 CG2 ga_26 CG1 CG2 CG3 ga_26 CG2 CG3 CG4 ga_26 CG3 CG4 CG5 ga_26 CG4 CG5 CB ga_26 [impropers] ;keep the planarity of the ring CB CG1 CG2 CG3 gi_1 CG1 CG2 CG3 CG4 gi_1 CG2 CG3 CG4 CG5 gi_1 CG3 CG4 CG5 CB gi_1 CG4 CG5 CB CG1 gi_1 CG5 CB CG1 CG2 gi_1 ;around CB CB CG1 CG5 CH gi_1 CB CG5 CH CG1 gi_1 CB CH CG1 CG5 gi_1 ;around CH CH CB +CH2CH2 gi_1 CH +CH2CH2 CB gi_1 CH CH2 CB +CH2gi_1 [dihedrals] ;in the chain - 3-fold CH2 CH +CH2+CH gd_16 CB CH +CH2+CH gd_16 -CH CH2 CH CB gd_16 -CH CH2 CH +CH2gd_16 ;around CH-CB - 2-fold CH2 CH CB CG5 gd_1 CH2 CH CB CG1 gd_1 +CH2CH CB CG5 gd_1 +CH2CH CB CG1 gd_1 ;around CB-CG - 2-fold?,do we need them? CH CB CG1 CG2 CH CB CG5 CG4 [ PSN ] [atoms] CH2 CH2 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0 CH3 CH3 0 0 [bonds] -CH CH2 gb_26 CH2 CH gb_26 CH CB gb_26 CB CG1 gb_15 CG1 CG2 gb_15 CG2 CG3 gb_15 CG3 CG4 gb_15 CG4 CG5 gb_15 CG5 CB gb_15 CH CH3 gb_26 [angles] -CH CH2
Re: [gmx-users] topology file for methane.
Hi, Justin: I am reading chapter 5 now. Still feel confused. I wrote methane.top file like this: ; Methane topology file ; ; The force field files to be included #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl METH 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_138 1METH C 1 -0.24 12.011 ; qtot 0.61 2 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 3 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 4 opls_140 1METH H 1 0.06 1.008 ; qtot 0.73 5 opls_140 1METH H 1 0.06 1.008 ; qtot 0.79 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name Methane [ molecules ] ; Compound#mols METH 1 ; ;;; Then I should go to ffoplsaa.rtp file to add a new molecule like : [METH] [ atoms ] Copls_135 -0.240 1 HC1opls_1400.060 1 HC2opls_1400.060 1 HC3opls_1400.060 1 HC4opls_1400.60 1 [ bonds ] C HC1 C HC2 C HC3 C HC4 ;;; Is that reasonable? Thanks for your help. On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: xianghong qi wrote: Hello, Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field? Thanks in advance. For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5. -Justin -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Some people make the world more special just by being in it. ___ 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] [Fwd: Problem in running energy minimization in gromacs]
Original Message Subject: Problem in running energy minimization in gromacs Date: Mon, 27 Oct 2008 15:16:23 + From: abhik mukhopadhyay [EMAIL PROTECTED] To: [EMAIL PROTECTED] Dear Dr. Spoel Good day. I am a beginner in Gromacs and having some problem in running energy minimization. I am working with an enzyme that has a Zn bound to four residues (3 cys and 1 his). I am trying to run a md simulation. But after the minimization I always found the Zinc coming out of the enzyme. I ran the minimization both with generating counter ions and without generating. The result is same. Do I need to take any special care to work with metalloenzyme ? Yes. You need restraints. Any suggestion from you will be highly useful for me. Best regards Abhik Mukhopadhyay -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology file for methane.
xianghong qi wrote: Hi, Justin: I am reading chapter 5 now. Still feel confused. I wrote methane.top file like this: ; Methane topology file ; ; The force field files to be included #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl METH 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_138 1METH C 1 -0.24 12.011 ; qtot 0.61 2 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 3 opls_140 1METH H 1 0.06 1.008 ; qtot 0.67 4 opls_140 1METH H 1 0.06 1.008 ; qtot 0.73 5 opls_140 1METH H 1 0.06 1.008 ; qtot 0.79 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp [ system ] ; Name Methane [ molecules ] ; Compound#mols METH 1 ; ;;; Then I should go to ffoplsaa.rtp file to add a new molecule like : [METH] [ atoms ] Copls_135 -0.240 1 HC1opls_1400.060 1 HC2opls_1400.060 1 HC3opls_1400.060 1 HC4opls_1400.60 1 [ bonds ] C HC1 C HC2 C HC3 C HC4 ;;; Is that reasonable? Thanks for your help. Seems fine to me. -Justin On Mon, Oct 27, 2008 at 1:54 PM, Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: xianghong qi wrote: Hello, Could anyone give me some suggestions about how to write a toplogy file for methane with OPLS-AA force field? Thanks in advance. For a very simple molecule like methane, it should be very straightforward to do from reading Chapter 5. -Justin -Xianghong Qi -- Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Some people make the world more special just by being in it. -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] H2O water density = 6.4617 g/l 1000 g/l
Chih-Ying Lin wrote: Hi I am creating the water box with the following command. The maxsol = 800; but # of SOL = 27; The H2O water density = 6.4617 g/l 1000 g/l Did I do anything wrong on my genbox command or 1w.gro file? Thank you Lin genbox -cp 1w.gro -cs 1w.gro -o box.gro -box 5 5 5 -maxsol 800 Output configuration contains 81 atoms in 27 residues Volume : 125 (nm^3) Density: 6.4617 (g/l) Number of SOL molecules: 27 Here is the 1w.gro 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 3 1SOL OW1.230.628.113 1SOLHW12.137.626.150 1SOLHW23.231.589.021 1.86206 1.86206 1.86206 So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you over-fill a cube of side length 5nm and get 27 water molecules. Use the standard water .gro files in the distribution and then minimize and equilibrate. Mark ___ 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] table command
He, Yang wrote: Hi all users, I just use the command mdrun -table table_nonbond.xvg to run the table file but it always shows that Fatal error: Tables in file table_nonbond.xvg not long enough for cut-off: should be at least 1.90 nm Actually, I have listed all the values up to 2.000nm in the file so I get a little confused about this error; Can anyone of you give me some suggestions? Compare your file with the ones in the distribution in share/gromacs/top/*xvg, or with those generated with mdrun -debug without attempting to use your own table. Mark ___ 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] table_bonded.xvg
Hi , I also encountered the same problem when I use the command: mdrun -table table_nonbond.xvg it shows that Fatal error: Library file bond_b0_b0.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) I wonder whether you have figured out this problem. Would you mind share your experience? Thank you . Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of A.Rzepiela [EMAIL PROTECTED] Sent: Monday, October 27, 2008 2:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] table_bonded.xvg Hi, When I type : mdrun -tableb bond_b0.xvg -v I get following message: Program mdrun, VERSION 4.0 Source code file: futil.c, line: 527 Fatal error: Library file bond_b0_b0.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) --- Thats what confused me when I type mdrun -tableb It reads table_b0.xvg Greetings Andrzej Hi, According to me it does not. I never change the default names. But with the default names the table file name option is table.xvg and for a tabulated bond table number 0, it correctly opens table_b0.xvg Berk From: A.Rzepiela at rug.nl To: gmx-users at gromacs.org Date: Fri, 24 Oct 2008 13:45:53 +0200 Subject: [gmx-users] table_bonded.xvg Dear Users In gromacs 4.0, in file force.c in function make_bonded_tables line (1007) sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1,_%s%d.%s, tabext, i, ftp2ext(efXVG)); produces table_bonded_bonded.xvg instead of table_bonded.xvg Greetings Andrzej Rzepiela ___ gmx-users mailing listgmx-users at 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-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users 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] table command
Hi Mark, Sorry to bother you again. I just change my table file a little by adding more values into the file and then I use the command; mdrun -table table_nonbond.xvg it shows : Fatal error: Library file tablep.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) What is the problem? Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL PROTECTED] Sent: Monday, October 27, 2008 3:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] table command He, Yang wrote: Hi all users, I just use the command mdrun -table table_nonbond.xvg to run the table file but it always shows that Fatal error: Tables in file table_nonbond.xvg not long enough for cut-off: should be at least 1.90 nm Actually, I have listed all the values up to 2.000nm in the file so I get a little confused about this error; Can anyone of you give me some suggestions? Compare your file with the ones in the distribution in share/gromacs/top/*xvg, or with those generated with mdrun -debug without attempting to use your own table. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to set up a rigid system
Dear GMX users, I am carrying out MD for a rigid system by Gromacs.But I couldnot know how to set up this rigid system. If you could give me some advice or some material, I will appreciate it. Jinyao Wang [EMAIL PROTECTED] 2008-10-28 ___ 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] mdrun doesn't run in version 4.0 on sgi server
I try to compile GROMACS with a combination of icc and ifort. Error occurs. These are the last lines of the compilation message: Making install in gmx_blas make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas' make[4]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas' make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_blas' Making install in gmx_lapack make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack' make[4]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack' make[4]: Nothing to be done for `install-exec-am'. make[4]: Nothing to be done for `install-data-am'. make[4]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack' make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib/gmx_lapack' make[3]: Entering directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib' /bin/sh ../../libtool --tag=CC --mode=compile /disk2/junwang/soft/intel/cc/10.1.018/bin/icc -DHAVE_CONFIG_H -I. -I../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\/disk2/junwang/soft/gromacs4/share/top\ -I/disk2/junwang/soft/fftw32_mpi/include -O3 -w -funroll-all-loops -MT libxdrf.lo -MD -MP -MF .deps/libxdrf.Tpo -c -o libxdrf.lo libxdrf.c /disk2/junwang/soft/intel/cc/10.1.018/bin/icc -DHAVE_CONFIG_H -I. -I../../src -I/usr/X11R6/include -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\/disk2/junwang/soft/gromacs4/share/top\ -I/disk2/junwang/soft/fftw32_mpi/include -O3 -w -funroll-all-loops -MT libxdrf.lo -MD -MP -MF .deps/libxdrf.Tpo -c libxdrf.c -o libxdrf.o libxdrf.c(112): error: identifier XDR_INT_SIZE is undefined cnt += XDR_INT_SIZE; ^ libxdrf.c(140): error: identifier XDR_INT_SIZE is undefined cnt += XDR_INT_SIZE; ^ compilation aborted for libxdrf.c (code 2) make[3]: *** [libxdrf.lo] Error 1 make[3]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib' make[2]: *** [install-recursive] Error 1 make[2]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src/gmxlib' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/disk2/junwang/soft/src/gromacs-4.0/src' make: *** [install-recursive] Error 1 My intel compiler versions are both 10.1.018. 2008/10/27 Mark Abraham [EMAIL PROTECTED] Carsten Kutzner wrote: Hi, Mark Abraham wrote: Lee Soin wrote: By invoking uname -a: Linux sgi4700 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux I don't know any other command to retrieve system information. Hmm, that looks like an SGI Altix 4700. IA64 kernels work on those machines. Well, not exactly. Ah, oops. I was thinking of the Altix 3700 series, which predates Montecito. My bad. They work in combination with Gromacs version = 3.3.x, but at least I have never managed to get them working with this year's CVS Gromacs or Gromacs 4.x - see also http://www.gromacs.org/pipermail/gmx-developers/2008-February/002405.html The strange thing is that these inner loops have not changed since 3.3.x, so the problem might be somewhere else. But actually the Fortran loops have a quite decent performance on that machine compared to assembly: In a single-CPU test I did with gmx 3.3 they were just about 10% slower. Good to know. Lee should definitely compare performance when using configure with and without --enable-fortran (and using --disable-cpu-optimization to avoid needing to set the environment variable). Mark ___ 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 -- Sun Li Department of Physics Nanjing University, China ___ 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] table command
He, Yang wrote: Hi Mark, Sorry to bother you again. I just change my table file a little by adding more values into the file and then I use the command; mdrun -table table_nonbond.xvg it shows : Fatal error: Library file tablep.xvg not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) What is the problem? It should mean what it says. I suspect either your command line or environment is different from before. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users]Simulated annealing
Dear Xavier and Jochen, Thank you for the suggestions: it works well now. Jes. On Mon, 27 Oct 2008 Xavier Periole wrote : On 27 Oct 2008 06:36:09 - JMandumpal [EMAIL PROTECTED] wrote: Dear GROMACS users, I have got a problem while running a simulated anealing simulations, using GROMACS 3.3.3 version, of pure water: the task: I want to cool the system (water- 500 molecules) from 360 K to 0K in 100ps time ( fast cooling). For that I used the following script: title= Water annealing simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps dt = 0.001; 1fs nsteps = 10 ; 1ps ; For exact run continuation or redoing part of a run init_step = 0 ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= SOL ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 ; 10ps nstvout = 1 ; 10ps nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 ; Output frequency for energies to log file and energy file nstlog = 0 nstenergy= 1000 ; 1ps ; Output frequency and precision for xtc file ;nstxtcout= 0 ;xtc-precision= 1000 ; select multiple groups. By default all atoms will be written. ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: pbc = xyz ; nblist cut-off rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb = 1.0 ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol optimize_fft = yes ; Relative dielectric constant for the medium epsilon_r= 1 ; for water ; Method for doing Van der Waals vdw-type = cut-off rvdw = 1.0 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; check for the range 0.1 to 0.15 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_geometry = 3d epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; OPTIONS FOR WEAK COUPLING ALGORITHMS in what follows you have commented out the temperature coupling details. I have never used SA but this for sure will not help the program controling the temperature! Put these back on should help! :)) ; Temperature coupling ;Tcoupl = berendsen ; Groups to couple separately ;tc-grps = system ; Time constant (ps) and reference temperature (K) ;tau-t = 0.1 ;ref-t= 360 ; simulated anealing annealing= single annealing_npoints= 2 annealing_time = 0 0 annealing_temp = 360 0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen-temp = 360 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 morse= no --- Problem: Having done the simulations, the output shows ( ener.edr , Temperature) a high temperature value around 850K. Clearly I did something wrong in my parameter file. --- the temperature extracted after the simulations --- s0 legend Temperature 0.00 376.058044 1.00 864.033020 2.00 873.607605 3.00 851.308838 4.00 847.223877 5.00 860.511841 6.00 813.547241 7.00 845.261658 8.00 872.090027 9.00 852.079468 10.00 849.152466 11.01 850.055237 12.01 834.468323 13.01 861.107300 14.01 828.380493 15.01 850.166809 16.00 850.382019 17.00 847.214478 18.00 851.201538 19.00 857.533691 20.00 849.760071 21.02 864.907715 22.02 837.307495 23.02 827.407593 24.02 841.464111 25.02 863.330688 26.02 841.096069 27.02 856.469910 28.02 854.449768 29.02 845.534973 30.02 853.421448 31.02 825.198059 32.00 857.317566 33.00 823.510925 34.00
