Re: [gmx-users] P4_error for extending coarse grained MD simulations
Hi Justin, what kind of error message do you get if you run this system on a single core without MPI? Carsten On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the state.cpt file using gmxdump and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: box-v (3x3) and thermostat-integral. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 chunleizhang@gmail.com写道： Information shown by gmxcheck: Checking file state.cpt # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file state_prev.cpt # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file md_360ns.trr trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: 张春雷 chunleizhang@gmail.com Date: Friday, June 25, 2010 16:46 Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. What does gmxcheck say about all the files involved? Mark Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin xwx...@gmail.com写道： How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I have searched the mail-list, but found no similar report. I also search through google, but no answer seems satisfactory. I once performed extending simulation for all atom simulation, and the method mentioned above worked. Is anyone familiar with
Re: [gmx-users] P4_error for extending coarse grained MD simulations
Hi Carsten, The error message I post is got on a single core with MPI. p0_6991: p4_error: interrupt SIGSEGV: 11 So it states p0_. I dont think the error is due to the MPI progrom. Am I right? Justin Zhang 在 2010年7月9日 下午4:00，Carsten Kutzner ckut...@gwdg.de写道： Hi Justin, what kind of error message do you get if you run this system on a single core without MPI? Carsten On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the *state.cpt* file using *gmxdump* and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: *box-v (3x3)* and *thermostat-integral*. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 chunleizhang@gmail.com写道： Information shown by gmxcheck: *Checking file state.cpt* # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 *Checking file state_prev.cpt* # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 *Checking file md_360ns.trr* trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: 张春雷 chunleizhang@gmail.com Date: Friday, June 25, 2010 16:46 Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. What does gmxcheck say about all the files involved? Mark Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin xwx...@gmail.com写道： How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I have searched the mail-list, but found no similar report. I also search through
Re: [gmx-users] P4_error for extending coarse grained MD simulations
On Jul 9, 2010, at 11:29 AM, 张春雷 wrote: Hi Carsten, The error message I post is got on a single core with MPI. p0_6991: p4_error: interrupt SIGSEGV: 11 So it states p0_. I dont think the error is due to the MPI progrom. Am I right? Yes, but there must be some more diagnostic information from mdrun about what has gone wrong. Please check stderr / stdout output files as well as md.log. Carsten Justin Zhang 在 2010年7月9日 下午4:00，Carsten Kutzner ckut...@gwdg.de写道： Hi Justin, what kind of error message do you get if you run this system on a single core without MPI? Carsten On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the state.cpt file using gmxdump and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: box-v (3x3) and thermostat-integral. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 chunleizhang@gmail.com写道： Information shown by gmxcheck: Checking file state.cpt # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file state_prev.cpt # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file md_360ns.trr trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: 张春雷 chunleizhang@gmail.com Date: Friday, June 25, 2010 16:46 Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. What does gmxcheck say about all the files involved? Mark Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin xwx...@gmail.com写道： How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded
Re: [gmx-users] P4_error for extending coarse grained MD simulations
Do you have same problem if you use the state_prec.cpt? Could it be just that file is corrupted for some reason ? On Jul 9, 2010, at 11:29 AM, 张春雷 wrote: Hi Carsten, The error message I post is got on a single core with MPI. p0_6991: p4_error: interrupt SIGSEGV: 11 So it states p0_. I dont think the error is due to the MPI progrom. Am I right? Justin Zhang 在 2010年7月9日 下午4:00，Carsten Kutzner ckut...@gwdg.de写道： Hi Justin, what kind of error message do you get if you run this system on a single core without MPI? Carsten On Jul 8, 2010, at 9:36 PM, 张春雷 wrote: Dear all, I have post this question about a two weeks ago. During these days, I followed suggestions from Mark and weixin, but did not fix it. Here, I repeat it again to seek more help. I attempt to extend MD simulation for a coarse-grained system. CG models are in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07. I tried to use check point file state.cpt to extend my simulation. The mdrun program can read to the check file. But it reported error like this: Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I check the state.cpt file using gmxdump and compare it with other checkpoint files that can be used for extending All-atom simulations. I found that in the CG check point file, some sections are missing: box-v (3x3) and thermostat-integral. I am not sure whether this missing sections cause my run crash. If it is, could any one tell me possible reasons that result in the loss of box-v and thermostat-integral and how to fix the problem? Your suggestions are greatly helpful and appreciated. Justin Zhang 在 2010年6月25日 下午4:45，张春雷 chunleizhang@gmail.com写道： Information shown by gmxcheck: Checking file state.cpt # Atoms 9817 Last frame -1 time 36.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file state_prev.cpt # Atoms 9817 Last frame -1 time 359010.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Checking file md_360ns.trr trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 # Atoms 9817 Reading frame2000 time 30.000 Item#frames Timestep (ps) Step 2401150 Time 2401150 Lambda2401150 Coords2401150 Velocities2401150 Forces 0 Box 2401150 Is anything wrong? 2010/6/25 Mark Abraham mark.abra...@anu.edu.au - Original Message - From: 张春雷 chunleizhang@gmail.com Date: Friday, June 25, 2010 16:46 Subject: Re: [gmx-users] P4_error for extending coarse grained MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org The last .gro file only provides coordinates of the system. No velocity is recorded. Actually, what I attempt to achieve is a binary identical trajectory. So I think the velocity from the last step is critical. I have tried another approach in which the checkpoint file is neglected. $mdrun_mpi_d -s md_720ns.tpr -e md_720ns.edr -o md_720ns.trr -g md_720ns.log It works. So the checkpoint file appears to contain some error. But it is generated by a normally finished production simulation. What does gmxcheck say about all the files involved? Mark Have you encountered similar things? Thank you for your suggestions! 在 2010年6月25日 上午9:16，weixin xwx...@gmail.com写道： How about using the last .gro file to continue your simulation? 2010/6/24 张春雷 chunleizhang@gmail.com Dear GMX-users, This is Justin. I am performing coarse-grained simulation on a protein-lipid bilayer system. This is a MARTINI CG model. I have successfully completed a 360ns simulation, during which the time step is 30 fs. I would like to extend the simulation to 1micro-second. The commands I used are: $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr $mdrun_mpi_d -s md_720ns.tpr -append -e md_360ns.edr -o md_360ns.trr -g md_360ns.log -cpi state.cpt However, I received the following message: Checkpoint file is from part 1, new output files will be suffixed part0002. Getting Loaded... Reading file md_720ns.tpr, VERSION 4.0.3 (double precision) Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010 Loaded with Money starting mdrun 'Protein in POPE bilayer' 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps). step 1200, remaining runtime: 0 s p0_6991: p4_error: interrupt SIGSEGV: 11 I have
[gmx-users] Ewald setting for hydrocarbon system?
Dear all, I need your favor. I have a hydrocarbon system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 4 ;ewald_rtol = 1e-5 ;optimize_fft = yes has been used for PME . Sofar I did not even include coulombtype=PME in my em.mdp file. What I had was: constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 200 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 Can you please guide me whether it is necessary to include these lines in em file for system having only partial charges like hydrocarbon (alkane). Also, in md.mdp file I have only coulombtype=PME and not the above Ewald settings. Do you recommend to include those settings? Without the mentioned lines I am getting reasonabel results (potential energy, kinetic, ,, also T coupling works perfectly). If I had better to unclude them what is the best value for fourierspacing? Thank you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Solvating protein
Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Solvating protein
On 10/07/2010 1:28 AM, Sai Pooja wrote: Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx. Mark Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Frozen N2 in a very long tube
Hear all, Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same thing or what is the reason for that. The system I simulated is nvt MD for N2 (with partial charge) diffusion in a long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a small cluster after a few ns. The weird thing is that I do not have such problem for either longer domain or short domain. The input parameters are: title= CNT ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 10 nstfout = 10 ; Checkpointing helps you continue after crashes nstcheckpoint= 10 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 1 xtc-precision= 100 ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 1 ref_t= 303.15 ; Pressure coupling Pcoupl = no Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 5 compressibility = 4.5e-5 ref_p= 1 ; Random seed for Andersen thermostat andersen_seed= 815131 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake
[gmx-users] fast rerun in order to get an energy
Hi, i will be grateful for any clue. Is it possible to extract an energy from finished trajectory? In my case the trajectory wasn't leading with flag e so it's obvious that I haven't got any edr files. I know that in log file there is some information about energy but I would like to have it in one file. My trajectory is quite long so that why I wouldn't like to start calcultations from the beginnig in order to achieve right files. If somebody had a similar situation then would be so kind and instruct me in right direction? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] fast rerun in order to get an energy
Magdalena wrote: Hi, i will be grateful for any clue. Is it possible to extract an energy from finished trajectory? In my case the trajectory wasn't leading with flag e so it's obvious that I haven't got any edr files. I know that in log file there is some information about energy but You didn't get an .edr file at all? Did you specify nstenergy 0 in the .mdp file? It seems odd that you didn't get anything. The .edr file is a standard output file, there is no need to specify any flag to cause it to be written. I would like to have it in one file. My trajectory is quite long so that why I wouldn't like to start calcultations from the beginnig in order to achieve right files. If somebody had a similar situation then would be so kind and instruct me in right direction? Thanks in advance You can pass your trajectory file to mdrun -rerun and it will recalculate the energies. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Solvating protein
Well thats the thing. I have checked my pdb files. All residues have either 0 or integer net charges. The number 0.994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained. I am using the charmm implemented version of gromacs. Pooja On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/07/2010 1:28 AM, Sai Pooja wrote: Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx. Mark Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Solvating protein
Sai Pooja wrote: Well thats the thing. I have checked my pdb files. All residues have There aren't charges in a .pdb file, unless you've somehow added them into one of the fields yourself. The file you need to check is your topology. A running value of the net charges is given in the [atoms] directive. Charges are assigned by pdb2gmx based on what is expected in the .rtp file and what you chose to assign in terms of protonation state. either 0 or integer net charges. The number 0.994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge genbox reads coordinate files, so I don't know how any charge it prints is meaningful. It tells me there is a zero charge on a lysozyme system that I know has a +8 charge (regardless of whether or not I pass it a topology as well), so don't believe genbox. Believe grompp. The magnitude is indeed due to small rounding errors. It should be interpreted as -1. -Justin when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained. I am using the charmm implemented version of gromacs. Pooja On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/07/2010 1:28 AM, Sai Pooja wrote: Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx. Mark Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] fast rerun in order to get an energy
I'm no expert but try a rerun, it will allow you to get at least the potential energies for each frame in your trr or xtc file, I've never been interested in kinetic for my reruns and as such am unsure how that would work though it should be possible. For this you'll need to build a slightly different mdp file with at least the following options (other stuff should be the same as in your initial run of this system) nsteps = 0 nxtenergy = 1 I usually turn the trr or xtc that I need to rerun into a gro file for input using trjconv -f traj.trr -o out.gro -ndec 3 You then need to grompp this new mdp file something like: grompp -f rerun.mpd -p topol.top -c out.gro and run an mdrun with the -rerun option turned on. mdrun -rerun traj.trr this should give you the energies at each frame in the normal ener.edr file used by g_energy May have missed something but this should be a good place to start looking, best of luck, Jeffery Perkins - Magdalena madle...@o2.pl wrote: Hi, i will be grateful for any clue. Is it possible to extract an energy from finished trajectory? In my case the trajectory wasn't leading with flag e so it's obvious that I haven't got any edr files. I know that in log file there is some information about energy but I would like to have it in one file. My trajectory is quite long so that why I wouldn't like to start calcultations from the beginnig in order to achieve right files. If somebody had a similar situation then would be so kind and instruct me in right direction? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Solvating protein
I checked topology file but going with grompp makes sense. Thank you. On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Well thats the thing. I have checked my pdb files. All residues have There aren't charges in a .pdb file, unless you've somehow added them into one of the fields yourself. The file you need to check is your topology. A running value of the net charges is given in the [atoms] directive. Charges are assigned by pdb2gmx based on what is expected in the .rtp file and what you chose to assign in terms of protonation state. either 0 or integer net charges. The number 0.994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge genbox reads coordinate files, so I don't know how any charge it prints is meaningful. It tells me there is a zero charge on a lysozyme system that I know has a +8 charge (regardless of whether or not I pass it a topology as well), so don't believe genbox. Believe grompp. The magnitude is indeed due to small rounding errors. It should be interpreted as -1. -Justin when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained. I am using the charmm implemented version of gromacs. Pooja On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 10/07/2010 1:28 AM, Sai Pooja wrote: Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx. Mark Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Solvating protein
Now I use genion and it says no ions to add? Using a coulomb cut-off of 1 nm No ions to add and no potential to calculate. command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o solions.gro -p finalnoss.top On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja saipo...@gmail.com wrote: I checked topology file but going with grompp makes sense. Thank you. On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: Well thats the thing. I have checked my pdb files. All residues have There aren't charges in a .pdb file, unless you've somehow added them into one of the fields yourself. The file you need to check is your topology. A running value of the net charges is given in the [atoms] directive. Charges are assigned by pdb2gmx based on what is expected in the .rtp file and what you chose to assign in terms of protonation state. either 0 or integer net charges. The number 0.994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge genbox reads coordinate files, so I don't know how any charge it prints is meaningful. It tells me there is a zero charge on a lysozyme system that I know has a +8 charge (regardless of whether or not I pass it a topology as well), so don't believe genbox. Believe grompp. The magnitude is indeed due to small rounding errors. It should be interpreted as -1. -Justin when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained. I am using the charmm implemented version of gromacs. Pooja On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.au wrote: On 10/07/2010 1:28 AM, Sai Pooja wrote: Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx. Mark Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Solvating protein
Sai Pooja wrote: Now I use genion and it says no ions to add? Using a coulomb cut-off of 1 nm No ions to add and no potential to calculate. command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o solions.gro -p finalnoss.top You haven't told genion to add anything. Use -np and/or -nn as appropriate. -Justin On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com wrote: I checked topology file but going with grompp makes sense. Thank you. On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Sai Pooja wrote: Well thats the thing. I have checked my pdb files. All residues have There aren't charges in a .pdb file, unless you've somehow added them into one of the fields yourself. The file you need to check is your topology. A running value of the net charges is given in the [atoms] directive. Charges are assigned by pdb2gmx based on what is expected in the .rtp file and what you chose to assign in terms of protonation state. either 0 or integer net charges. The number 0.994 seems like a rounding off error especially since the output of genbox says that the system has zero net charge. Again, I encounter this no-zero net charge genbox reads coordinate files, so I don't know how any charge it prints is meaningful. It tells me there is a zero charge on a lysozyme system that I know has a +8 charge (regardless of whether or not I pass it a topology as well), so don't believe genbox. Believe grompp. The magnitude is indeed due to small rounding errors. It should be interpreted as -1. -Justin when I run grompp with an mdp file for energy minimization with the protein( excluding hydrogen ) restrained. I am using the charmm implemented version of gromacs. Pooja On Fri, Jul 9, 2010 at 11:49 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/07/2010 1:28 AM, Sai Pooja wrote: Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.. NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.94e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? I'd believe grompp before genbox. Surely you know already what is in your system, and thus its total charge. You should already know the protonation state of all of your relevant protein residues, because you made choices for them with pdb2gmx. Mark Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Quaerendo Invenietis-Seek and you shall discover. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
Re: [gmx-users] fast rerun in order to get an energy
Reruns MUST use trr files. On Jul 9, 2010, at 19:04, Jeffery Perkins jeffery.perk...@ufv.ca wrote: I'm no expert but try a rerun, it will allow you to get at least the potential energies for each frame in your trr or xtc file, I've never been interested in kinetic for my reruns and as such am unsure how that would work though it should be possible. For this you'll need to build a slightly different mdp file with at least the following options (other stuff should be the same as in your initial run of this system) nsteps = 0 nxtenergy = 1 I usually turn the trr or xtc that I need to rerun into a gro file for input using trjconv -f traj.trr -o out.gro -ndec 3 You then need to grompp this new mdp file something like: grompp -f rerun.mpd -p topol.top -c out.gro and run an mdrun with the -rerun option turned on. mdrun -rerun traj.trr this should give you the energies at each frame in the normal ener.edr file used by g_energy May have missed something but this should be a good place to start looking, best of luck, Jeffery Perkins - Magdalena madle...@o2.pl wrote: Hi, i will be grateful for any clue. Is it possible to extract an energy from finished trajectory? In my case the trajectory wasn't leading with flag e so it's obvious that I haven't got any edr files. I know that in log file there is some information about energy but I would like to have it in one file. My trajectory is quite long so that why I wouldn't like to start calcultations from the beginnig in order to achieve right files. If somebody had a similar situation then would be so kind and instruct me in right direction? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] information regarding the bootstrap method implemented with the g_wham
Hi all, I am trying to understand how the bootstrap method has been implemented within the g_wham. Unfortunately, it is poorly documented in the help menu and in the manual. I could not track of the options regarding the method. Could anyone (maybe the one who has implemented the method) give a little bit detailed information, please? Thanks in advance -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Missing sugar atom in CHARMM dna.rtp
Hi In the gromacs git version, I noticed that the sugar atom O2' is missing from the dna.rtp file... Best wishes George-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Missing sugar atom in CHARMM dna.rtp
Patargias, George wrote: Hi In the gromacs git version, I noticed that the sugar atom O2' is missing from the dna.rtp file... No problem there, for deoxyribose. -Justin Best wishes George-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdp file settings for PME
Dear experts, I posted this message before but I think you did not see it since I noticed messages after this have been replied. I have a hydrocarbon system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 4 ;ewald_rtol = 1e-5 ;optimize_fft = yes has been used for PME . Sofar I did not even include coulombtype=PME in my em.mdp file. What I had was: constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 200 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 Can you please guide me whether it is necessary to include these lines in em file for system having only partial charges like hydrocarbon (alkane). Also, in md.mdp file I have only coulombtype=PME and not the above Ewald settings. Do you recommend to include those settings? Without the mentioned lines I am getting reasonabel results (potential energy, kinetic, ,, also T coupling works perfectly). If I had better to unclude them what is the best value for fourierspacing? Thank you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx with DNA
Thanks for your reply Justin. I am trying to generate a topology dor a dna structure using the charmm dna.rtp I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for the 5' and 3' ends I got this error Fatal error: atom N not found in buiding block 2DG while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I quess I need to change something in the .rtp and/or the .tdb files. But what? Thanks a lot George-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Installing gromacs from git
Hi, I had used the following steps to install a git version of gromacs. It installed correctly and I have been using it for a while. However, even though I didnt install the parallel version, when I use mdrun it runs in parallel. Is installation in the parallel mode by default? Is there a way to use it without parallelization? 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install Pooja On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: Sai Pooja wrote: For future reference, I was able to install gromacs and this is what finally worked - installing gromacs in a folder different than the untared. It somehow helped to not create the folder but just directly using the name in the prefix 301 cd gromacs 302 ls 303 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 304 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 305 clear 306 ls 307 ./configure --help 308 ./configure --prefix=/fs/home/sm868/gromacsnew 309 make log 310 ls 311 jmacs log 312 grep error log 313 grep Error log 314 make install I got the msg - GROMACS is installed under /fs/home/sm868/gromacsnew. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and possibly LD_LIBRARY_PATH or /etc/ld.so.conf if you are using dynamic libraries. Thanks for the help. *One question - There is already another version of gromacs installed in the /usr/local so I used a different directory to install it. Now do I need to use make links?* Do you normally make links? If so, you'll be over-writing the executables in /usr/local/bin. One other possible side effect is that if both /usr/local/bin and /usr/local/gromacs/bin are in your $PATH, you can't define which executable to use unambiguously without specifying the whole path name for each executable. If you're using several version of Gromacs concurrently on the same machine, it's probably best to just install them in their own locations and source the proper GMXRC when you log in to use the version you want. -Justin * * Pooja On Sun, Jun 20, 2010 at 2:17 AM, Sai Pooja saipo...@gmail.com mailto: saipo...@gmail.com wrote: I redid the entire thing after that first mail in which i reported the error related to fftw(including running the make uninstall commands and removing the folders entirely and getting fresh ones). I apologize for not specifying this and like I said... there seemed to be no errors this time except when I ran make install for gromacs. The error looks like this: make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: *** [install-recursive] Error 1 I didn't find any other error.. is there a way to look for them other than looking at what is being printed while the command is running? I tried $ grep Error */* in the folder but found nothing more than entries in different scripts etc. On Sun, Jun 20, 2010 at 1:27 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: - Original Message - From: Sai Pooja saipo...@gmail.com mailto:saipo...@gmail.com Date: Sunday, June 20, 2010 15:09 Subject: Re: [gmx-users] Installing gromacs from git To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org History log: 189 ./configure --enable-threads --enable-float --prefix=/fs/home/sm868/fftw-3.2.2 190 make 191 clear 192 make install 193 cd .. 194 cd gromacs 195 ls 196 export CPPFLAGS=-I/fs/home/sm868/fftw-3.2.2/include 197 export LDFLAGS=-L/fs/home/sm868/fftw-3.2.2/lib 198 ./bootstrap 199 ls 200 ./configure --prefix=/fs/home/sm868/gromacs 201 make 202 make install Everything works till I get the following error with make install(after it runs for a while) : make[3]: *** [install-man1] Error 1 make[3]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/fs/home/sm868/gromacs/man/man1' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/fs/home/sm868/gromacs/man' make: ***
Re: [gmx-users] pdb2gmx with DNA
Patargias, George wrote: Thanks for your reply Justin. I am trying to generate a topology dor a dna structure using the charmm dna.rtp I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 for the 5' and 3' ends I got this error Fatal error: atom N not found in buiding block 2DG while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I quess I need to change something in the .rtp and/or the .tdb files. But what? Maybe, maybe not. It looks like pdb2gmx is trying to treat your DNA as protein. What is your command line? What are you choosing for termini? -Justin Thanks a lot George-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mdp file settings for PME
jojo J wrote: Dear experts, I posted this message before but I think you did not see it since I noticed messages after this have been replied. I have a hydrocarbon Messages do not receive replies in any sort of order. Probably no one has had any relevant comments yet, or they live in a time zone where they are not awake :) system with no charged particles. Today In one of the GROMACS tutorials I saw the following setting in em.mdp file: fourierspacing = 0.12 ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 4 ;ewald_rtol = 1e-5 ;optimize_fft = yes has been used for PME . Sofar I did not even include coulombtype=PME in my em.mdp file. What I had was: constraints = all-bonds integrator = steep dt = 0.002; ps ! nsteps = 200 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; ; Energy minimizing stuff ; emtol = 1000.0 Can you please guide me whether it is necessary to include these lines in em file for system having only partial charges like hydrocarbon (alkane). Also, in md.mdp file I have only coulombtype=PME and not the This contradicts your statement above. You said you had only uncharged particles, but clearly this is not the case. above Ewald settings. Do you recommend to include those settings? For energy minimization, the effects of plain cutoffs may or may not be significant. Using plain cutoffs for actual simulation is a bad idea. The artifacts are well-documented and for modern simulations any good reviewer should raise an immediate concern if plain cutoffs were used and not thoroughly justified. A method like PME is significantly more accurate, but you can also achieve reasonable results using switch, shift, etc. Read about the relevant mechanics of the force field you're using for what might be appropriate. Without the mentioned lines I am getting reasonabel results (potential energy, kinetic, ,, also T coupling works perfectly). If I had better to unclude them what is the best value for fourierspacing? I don't think there's ever been any sort of systematic study on the effects of Fourier grid spacing. The trade-off is between speed and accuracy. Larger values speed up calculations, but make PME less accurate. Smaller values have the opposite effect. You could do a small test for yourself (0.12, 0.16, 0.18...) to see if there are any adverse effects. -Justin Thank you, -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the Pressure control in GROMACS 4.0.7
Dear users, I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure value fluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressure sometimes is much larger than what I have set,for example, I have set ref_p = 1.0 , but the average is actually over 7 bar. It is because I have not set properly , or something else? Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the Pressure control in GROMACS 4.0.7
zhongjin wrote: Dear users, I think the pressure control in gromacs 4.0.7 may have some problems. First ,The pressure value fluctuates widely ,even between -7984.377930 and 5920.053711 bar.Second,the average pressure sometimes is much larger than what I have set,for example, I have set ref_p = 1.0 , but the average is actually over 7 bar. It is because I have not set properly , or something else? In the absence of your .mdp file and a more detailed description of your system, extent of equilibration, etc it's hard to make any judgment. Wide fluctuations are not uncommon in relatively small systems: http://www.gromacs.org/Documentation/Terminology/Pressure -Justin Zhongjin He -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
