[gmx-users] Fwd: [gmx-developers] Simulated annealing problem
This is a user problem, not a development problem. Original Message Subject: [gmx-developers] Simulated annealing problem Date: Thu, 14 Mar 2013 10:15:39 +0530 From: Gaurav Jerath g.jer...@iitg.ernet.in Reply-To: Discussion list for GROMACS development gmx-develop...@gromacs.org To: gmx-develop...@gromacs.org Hi, I am trying to anneal two protein molecules. The usual protocol for a MD simulation was followed. But the problem arises that at high temperatures, the number of hydrogen bonds are increasing instead of getting decreased. The GROMOS43a1 force field was used and the mdp file for the simulation is shown below: ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002;ps ! nsteps = 500 ; total 10ns. ;nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein non-Protein; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 2.75 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 310 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 ; SIMULATED ANNEALING CONTROL = annealing = periodic periodic annealing_npoints= 3 3 annealing_time = 0 5000 1 0 5000 1 annealing_temp = 300 500 300 300 500 300 Kindly help me as I am unable to figure out if there is a problem in my parameters file -- gmx-developers mailing list gmx-develop...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulated annealing problem
Hi, I am trying to anneal two protein molecules. The usual protocol for a MD simulation was followed. But the problem arises that at high temperatures, the number of hydrogen bonds are increasing instead of getting decreased. The GROMOS43a1 force field was used and the mdp file for the simulation is shown below: ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002;ps ! nsteps = 500; total 10ns. ;nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Proteinnon-Protein; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Energy monitoring energygrps = Protein SOL ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 2.75 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 310 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 ; SIMULATED ANNEALING CONTROL = annealing = periodic periodic annealing_npoints= 3 3 annealing_time = 0 5000 1 0 5000 1 annealing_temp = 300 500 300 300 500 300 Kindly help me as I am unable to figure out if there is a problem in my parameters file -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD in Vacuum
Hi, You also need to consider the ensemble you want to investigate. If you simulate under constant energy you need a shorter timestep than you would have in solution and probably double precision. In the articles I list below we used a timestep of 0.5 fs and 1 fs, respectively, and double precision. Monitor the total energy and you will see it drifting early on if you e.g. have a timestep that is too long. You could also try to apply the constraints more accurately than default. * Patriksson, A., Marklund, E., and Van der Spoel, D. (2007) Protein Structures under Electrospray Conditions. Biochemistry, 56(4):933pp * Marklund, E. G., Larsson, S. D., Patriksson, A., Van der Spoel, D., and Caleman, C. (2009) Structural stability of electrosprayed proteins: temperature and hydration effects. Physical Chemistry Chemical Physics, 11(36):8069pp Modesto Orozco and coworkers have also simulated biomolecules in the gas phase. I suggest to also have a look at their work. Best, On Mar 13, 2013, at 8:22 PM, Justin Lemkul wrote: On 3/13/13 12:53 PM, Lara Bunte wrote: Hello In all my tutorials for md they investigate a molecule in solution. I want to do md simulations in vacuum and I did not find a good tutorial. So I want to ask you what should I do for a md simulation in vaccum? Consult the literature. Tutorials will not cover every topic, and since most MD force fields were designed for condensed-phase simulations, it's awfully hard to explain to a new user why we're making wild changes to normal settings and hope that they understand :) I take a molecule, optimize the structure, generate a topology with gromacs and what after this? Do I also have to make a box? what is the procedure? Usually in vacuo simulations are done in the absence of periodicity and with infinite cutoffs. In general, an approach like the following is used: comm-mode = Angular nstlist = 0 rlist = 0 rvdw = 0 rcoulomb = 0 pbc = no ns-type = simple vdwtype = cutoff coulombtype = cutoff Check literature to be sure to establish a protocol with some basis in precedent. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] position restraints
Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] position restraints
Restraints allow, by definition, for slight deviations. Erik On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote: Dear gmx users, I want to use restraints on backbone of my protein to keep its secondary structure during minimization and equilibration steps. To do so, I generated backbone-restrain.itp and then included it to top file. Next, added define = -DPOSRES to minim.mdp file. After minimization, when I check the minimization output file, I saw that the backbone of input and output files are not exactly the same. Is there any step which I have not done to set the restraints correctly? Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query for gromacs-4.5.4
Hello Sir, The job runs for 8 processes given 1 , 2 or 8 nodes but not for more than that. 16 proceses : Segmentation fault and For 32 processes it gives : Fatal error : 467 particles communicated to PME node 4 are more than 2/3 times the cut off out of the domain decomposition cell of their charge group in deimesion x. This usually means that your system is not well equilibrated What can be the reason... Thanks, Chaitali On Tue, Mar 12, 2013 at 3:50 PM, Mark Abraham mark.j.abra...@gmail.comwrote: It could be anything. But until we see some GROMACS diagnostic messages, nobody can tell. Mark On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre chaitujo...@gmail.com wrote: Sir, Thanks for your reply But the same script runs on some other cluster with apprx same configuration but not on cluster on which I am doing set up. Also job hangs after some 16000 steps but not come out immediately. It might be problem with configuration or what? Thanks... Chaitali On Tue, Mar 12, 2013 at 2:18 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're just MPI error messages and don't provide any useful GROMACS diagnostics. Look in the end of the .log file, stderr and stdout for clues. One possibility is that your user's system is too small to scale effectively. Below about 1000 atoms/core you're wasting your time unless you've balanced the load really well. There is a simulation-system-dependent point below which fatal GROMACS errors are assured. Mark On Tue, Mar 12, 2013 at 6:17 AM, Chaitali Chandratre chaitujo...@gmail.comwrote: Hello Sir, Actually I have been given work to setup gromacs-4.5.4 in our cluster which is being used by users.I am not gromacs user and not aware of its internal details. I have got only .tpr file from user and I need to test my installation using that .tpr file. It works fine for 2 nodes 8 processes , 1 node 8 processes. But when number of processes are equal to 16 it gives segmentation fault and if number of processes are equal to 32 it gives error message like HYD_pmcd_pmiserv_send_signal (./pm/pmiserv/pmiserv_cb.c:221): assert (!closed) failed ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:128): unable to send SIGUSR1 downstream HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:388): error waiting for event [ main (./ui/mpich/mpiexec.c:718): process manager error waiting for completion I am not clear like whether problem is there in my installation or what? Thanks and Regards, Chaitalij On Wed, Mar 6, 2013 at 5:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/6/13 4:20 AM, Chaitali Chandratre wrote: Dear Sir , I am new to this installation and setup area. I need some information for -stepout option for What more information do you need? mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4. (my node having 64 GB mem running with 16 processes, nsteps = 2000) There are too many causes to name. Please consult http://www.gromacs.org/ **Documentation/Terminology/**Blowing_Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you need further help, please be more specific, including a description of the system, steps taken to minimize and/or equilibrate it, and any complete .mdp file(s) that you are using. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the
[gmx-users] Re: Gromacs-4.6 installation on cygwin problem
Mr M. Thanks a lot for your help... I will contact you if I get any problem. -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-4-6-installation-on-cygwin-problem-tp5006297p5006319.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query for gromacs-4.5.4
One cannot run an arbitrary simulation on an arbitrary number of processors. The particles in the simulation have to get mapped to processors that handle them. This is done in small parcels called domains. The atoms move between domains, and so the responsibility moves too. If the velocities are high with respect to the size of the domains, the responsibility might shift too far for the implementation to handle. This is happening here. GROMACS does not handle arbitrary redistribution of particles to processors because the algorithm to do that would be too expensive for the normal case where the redistribution is more orderly. So either the velocities are too high (the system is not well equilibrated), and you are getting lucky on small numbers of nodes that the domains are big enough to cope with the equilibration process, or you are trying to use domains that are just too small for normal velocities. We'd need to know what's in the .tpr to have an opinion about what a reasonable maximum number of nodes might be, but a simulation with less than a thousand atoms per processor starts having to pay attention to these issues. Mark On Thu, Mar 14, 2013 at 1:25 PM, Chaitali Chandratre chaitujo...@gmail.comwrote: Hello Sir, The job runs for 8 processes given 1 , 2 or 8 nodes but not for more than that. 16 proceses : Segmentation fault and For 32 processes it gives : Fatal error : 467 particles communicated to PME node 4 are more than 2/3 times the cut off out of the domain decomposition cell of their charge group in deimesion x. This usually means that your system is not well equilibrated What can be the reason... Thanks, Chaitali On Tue, Mar 12, 2013 at 3:50 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It could be anything. But until we see some GROMACS diagnostic messages, nobody can tell. Mark On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre chaitujo...@gmail.com wrote: Sir, Thanks for your reply But the same script runs on some other cluster with apprx same configuration but not on cluster on which I am doing set up. Also job hangs after some 16000 steps but not come out immediately. It might be problem with configuration or what? Thanks... Chaitali On Tue, Mar 12, 2013 at 2:18 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're just MPI error messages and don't provide any useful GROMACS diagnostics. Look in the end of the .log file, stderr and stdout for clues. One possibility is that your user's system is too small to scale effectively. Below about 1000 atoms/core you're wasting your time unless you've balanced the load really well. There is a simulation-system-dependent point below which fatal GROMACS errors are assured. Mark On Tue, Mar 12, 2013 at 6:17 AM, Chaitali Chandratre chaitujo...@gmail.comwrote: Hello Sir, Actually I have been given work to setup gromacs-4.5.4 in our cluster which is being used by users.I am not gromacs user and not aware of its internal details. I have got only .tpr file from user and I need to test my installation using that .tpr file. It works fine for 2 nodes 8 processes , 1 node 8 processes. But when number of processes are equal to 16 it gives segmentation fault and if number of processes are equal to 32 it gives error message like HYD_pmcd_pmiserv_send_signal (./pm/pmiserv/pmiserv_cb.c:221): assert (!closed) failed ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:128): unable to send SIGUSR1 downstream HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:388): error waiting for event [ main (./ui/mpich/mpiexec.c:718): process manager error waiting for completion I am not clear like whether problem is there in my installation or what? Thanks and Regards, Chaitalij On Wed, Mar 6, 2013 at 5:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/6/13 4:20 AM, Chaitali Chandratre wrote: Dear Sir , I am new to this installation and setup area. I need some information for -stepout option for What more information do you need? mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4. (my node having 64 GB mem running with 16 processes, nsteps = 2000) There are too many causes to name. Please consult http://www.gromacs.org/ **Documentation/Terminology/**Blowing_Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you need further help, please be more specific, including a description of the system, steps taken to minimize and/or equilibrate it,
[gmx-users] template parallelization
First, here my system : Cent Os 64 bits gcc : 4.4.6 fftw : 3.3.2 including SSE 2 I am writing a code to find out the number of five and six membered rings in structure I of hydrate . My code takes long time to compile for my 500ps trajectory . So my query is that can the template file be made to run in parallel fashion ? If so ,how -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: TMD using free energy code
I have done a test for a TMD between two conformations of a POPC in water with this mdp file: define = -DPOSRES_TMD ; POSRES-TMD defined in the top file and including only the heavy atom of POPC refcoord-scaling = all cpp= /usr/bin/cpp constraints = hbonds constraint_algorithm = LINCS integrator = md dt = 0.002 nsteps = 5 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 500 nstlist = 5 ns_type = grid coulombtype = PME rlist = 1 rcoulomb= 1 rvdw= 1 ; Berendsen temperature coupling Tcoupl = v-rescale tau_t = 0.1 0.1 tc_grps = POPC SOL ref_t = 300 300 ; Pressure coupling Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 0.5 ref_p = 1 compressibility = 4.5e-05 unconstrained_start = yes gen_vel = no gen_temp= 300 gen_seed= 173529 optimize_fft= yes ; free-energy free_energy = yes init_lambda = 0.0 delta_lambda = 0 and these commands : grompp -f TMD.mdp -c begin.gro -p topol.top -o tmd.tpr -n index.ndx -r begin.gro -rb end.gro mdrun -v -deffnm tmd Nevertheless, it doesn't work even with non-zero value for delta_lambda. I don't know which free energy options I have to modify. Indeed, according to the manual, the other options are tuned for FEP or TI. Any help would be greatly appreciated. Landraille PS : I use v4.5.5. Indeed, with the v4.6, mdrun doesn't start and I have the error message Function type U-B not implemented in ip_pert. -- View this message in context: http://gromacs.5086.n6.nabble.com/TMD-using-free-energy-code-tp5006260p5006321.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] template parallelization
Do you really mean compile time? If so, issue make -j X (where x is the number of jobs used for building). If you mean runtime then the easiest thing is to split your trajectory in parts and run the processes in parallel, then patch the results together. That's if the calculations can be done on a per-frame basis (i.e. embarrassingly parallelizable problems). Next in line is to wrap some performance critical loop(s) in OpenMP pragmas and link to the OpenMP libraries on your system. If you want others to benefit from the code you should adhere to the parallelization framework in gromacs, e.g. use gromacs' wrappers and preprocessor directives for OpenMP and MPI magic. The latter may be more trouble than it's worth if your analysis is only for a limited userbase. There is a framework underway in gromacs for parallel analysis tools, but as far as I know it's not finalized yet. Erik On Mar 14, 2013, at 2:22 PM, subhadipdas wrote: First, here my system : Cent Os 64 bits gcc : 4.4.6 fftw : 3.3.2 including SSE 2 I am writing a code to find out the number of five and six membered rings in structure I of hydrate . My code takes long time to compile for my 500ps trajectory . So my query is that can the template file be made to run in parallel fashion ? If so ,how -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: template parallelization
Sorry but i can't understand the part about parallelization framework in gromacs . Can you please elaborate on this -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320p5006323.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: template parallelization
Gromacs currently use OpenMP and/or MPI with it's own wrappers for parallel computation. There is a general framework being developed for parallelizing analysis tools, but I don't know the specifics and I beleive it's not ready for use yet. Is that helping you? Erik On Mar 14, 2013, at 3:20 PM, subhadipdas wrote: Sorry but i can't understand the part about parallelization framework in gromacs . Can you please elaborate on this -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320p5006323.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: template parallelization
Thanks for the reply . Looks like it is not a layman's problem but the reply u sent me has given me the idea where to start . -- View this message in context: http://gromacs.5086.n6.nabble.com/template-parallelization-tp5006320p5006325.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] bonding energy
I would check the energy connection between an amino acid and a ligand. After simulation, I run the following command: g_dist_mpi -f x.trr -s x.tpr -n index.ndx -o pro.xvg Then I choose the bond option (option 1) from the proposed options. Is this true for energy bonding finding between two molecules? thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] bonding energy
On 3/14/13 4:08 PM, fatemeh ramezani wrote: I would check the energy connection between an amino acid and a ligand. After simulation, I run the following command: g_dist_mpi -f x.trr -s x.tpr -n index.ndx -o pro.xvg Then I choose the bond option (option 1) from the proposed options. Is this true for energy bonding finding between two molecules? g_dist has nothing to do with bonds, so what you've posted doesn't make any sense. There will be no bonding energy between two species that do not have actual chemical bonds defined in the topology, and even then, an .edr file (analyzed using g_energy) does not have decomposed bonding terms for individual interactions. Gromacs just doesn't work like that. You can get the sum of nonbonded interactions by setting appropriate energygrps in the .mdp file, and there are some rather complex methods for getting bonded energies (i.e. subset .tpr and .trr/.xtc, use mdrun -rerun on only those atoms of interest), but often such quantities are not particularly useful. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] polymer duplicate atoms
Hi I use the pdb2gmx to generate topology file of polymer f2311(fluororubber) with the incorrect information of GROMACS structural file (conf.gro). There are 680 atoms in my input (.pdb) file. But, 660 atoms are deleted in conf.gro file because of duplicate atoms. The printed message as follow: http://gromacs.5086.n6.nabble.com/file/n5006328/info.jpg Residues Fre, Fbg and Fen denote repeat unit., head and tail part of polymer, respectively. How can I obtain the correct file structure (conf.gro) to avoid deleting duplicate atoms. Any help with my best appreciation. Attachment is my pdb file. f2311.pdb http://gromacs.5086.n6.nabble.com/file/n5006328/f2311.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-tp5006328.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] polymer duplicate atoms
The residue number is not incrementing in your coordinate file (it stays as 1), so it thinks it is all the same residue. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of cqgzc Sent: Friday, 15 March 2013 12:17 PM To: gmx-users@gromacs.org Subject: [gmx-users] polymer duplicate atoms Hi I use the pdb2gmx to generate topology file of polymer f2311(fluororubber) with the incorrect information of GROMACS structural file (conf.gro). There are 680 atoms in my input (.pdb) file. But, 660 atoms are deleted in conf.gro file because of duplicate atoms. The printed message as follow: http://gromacs.5086.n6.nabble.com/file/n5006328/info.jpg Residues Fre, Fbg and Fen denote repeat unit., head and tail part of polymer, respectively. How can I obtain the correct file structure (conf.gro) to avoid deleting duplicate atoms. Any help with my best appreciation. Attachment is my pdb file. f2311.pdb http://gromacs.5086.n6.nabble.com/file/n5006328/f2311.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms- tp5006328.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Salt bridge analysis tool
Hi, I am trying to analyse my trajectory for specific salt bridges and the only program I can find is g_saltbr with the -sep command, which gives back all atom pairs that come within the set cutoff at any point in simulation time, whether they are charged and H-bond partners or not and regardless of whether they are together long enough or just glancing past each other. This means that I am getting 80 000+ salt bridges in my protein, which is obviously incorrect. I cannot find any other program to analyse salt bridges, does anyone know if there is a better one? Or if there is a way to make g_saltbr's results more specific and managable. Thank you very much for your consideration. Regards, -- View this message in context: http://gromacs.5086.n6.nabble.com/Salt-bridge-analysis-tool-tp5006330.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Salt bridge analysis tool
On 3/14/13 10:14 PM, albielyons wrote: Hi, I am trying to analyse my trajectory for specific salt bridges and the only program I can find is g_saltbr with the -sep command, which gives back all atom pairs that come within the set cutoff at any point in simulation time, whether they are charged and H-bond partners or not and regardless of whether they are together long enough or just glancing past each other. This means that I am getting 80 000+ salt bridges in my protein, which is obviously incorrect. I cannot find any other program to analyse salt bridges, does anyone know if there is a better one? Or if there is a way to make g_saltbr's results more specific and managable. tpbconv -zeroq can be used to zero out charges on groups that are not of interest, thereby reducing the number of charge pairs that can be detected. g_dist can also be used to measure distances between specific groups that you are interested in. Either approach requires creation of index groups that specify groups of interest. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
