Re: [gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko)
Actually I am not sure that I can understand what is thread. But I can paste QMMM file here: title= my_mdp_file cpp = /usr/bin/cpp -traditional include = define = integrator = md tinit= 0 dt = 0.0005 nsteps = 2000 init_step= 0 comm-mode= Linear nstcomm = 1 comm_grps= system emtol= 100.0 emstep = 0.0005 nstxout = 100 nstvout = 100 nstfout = 100 ; Checkpointing helps you continue after crashes nstcheckpoint= 100 nstlog = 10 nstenergy= 10 nstxtcout= 10 ;xtc-precision= 1000 ;xtc_grps = DNA nstlist = 5 ns_type = grid pbc = xyz rlist= 1.4 domain-decomposition = no coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation ;fourierspacing= 0.16; grid spacing for FFT ;coulombtype = Cut-off ;rcoulomb-switch = 0 rcoulomb = 1.4 epsilon_r= 1 epsilon_rf = 1 vdwtype = Cut-Off rvdw-switch = 0. rvdw = 1.4 DispCorr = No fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ;pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no tcoupl = V-rescale tc-grps = LIG SOL tau-t= 0.1 0.1 ref-t= 309 309 Pcoupl = Berendsen Pcoupltype = Isotropic tau-p= 1.0 compressibility = 4.5e-5 ref-p= 1.0 QMMM = yes QMMM-grps= QMatoms QMmethod = DFT QMMMscheme = ONIOM QMbasis = sto-3g QMcharge = 0 QMmult = 1 gen_vel = no gen_temp = 00 gen_seed = 18111976 constraints = all-bonds constraint_algorithm = LINCS unconstrained_start = no Shake-SOR= no shake_tol= 0.0001 lincs_order = 4 lincs-iter = 1 lincs_warnangle = 30 morse= no 2010/12/7 Gerrit Groenhof ggro...@gwdg.de Dera gromacs users, I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2. When I run DFT I got an error: number of CPUs for gaussian = 1 memory for gaussian = 5000 accuracy in l510 = 8 NOT using cp-mcscf in l1003 Level of SA at start = 0 Segmentation fault Are you trying to use more than one thread? Gerrit Please could you advice me on this? 6. QMMM, Segmentation fault (Olga Ivchenko) -- 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] group temperatures and kinetic energies
Dear gmx'ers, I am somewhat confused relating temperatures and kinetic energies in gromacs output. I simulate NVE system of N0 rigid molecules in vacuo, 'comm_mode' is set to 'None'. When I check the output 'Kinetic En.' and 'Temperature', the relation between them (see Eq. (3.13) of Manual) corresponds to 6*N0 degrees of freedom, that's OK. Then the system is divided into two groups with N1 and N0-N1 molecules. While reruning the simulation (with 'energygrps' option), the energies of both groups are written to energy file, and the output includes also 'Temp_group1' and 'Temp_group2'. My wish is to obtain separate kinetic energies of the groups. I try to calculate them using for group degrees of freedom 6*N1 and 6*(N0-N1) values, resp. The problem is that the sum of instantaneous group kinetic energies is not equal to full 'Kinetic En.'! I could suppose that it is due to some relative motion of the groups, but the difference in energies through the simulation may be both positive and negative. What is the real source of this difference? Thanks in advance, -- Regards, Dmitri mailto:ddu...@ngs.ru-- 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] group temperatures and kinetic energies
I'm awfully sorry for groundless troubling! The sum of group kinetic energies IS STRONGLY EQUAL to the total one. Really I did compared the outputs of DIFFERENT simulations... Dear gmx'ers, I am somewhat confused relating temperatures and kinetic energies in gromacs output. I simulate NVE system of N0 rigid molecules in vacuo, 'comm_mode' is set to 'None'. skip What is the real source of this difference? -- Regards, Dmitri mailto:ddu...@ngs.ru-- 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] trouble parallelizing a simulation over a cluster
Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing list members; I have been trying to run a simulation on a computer cluster for the first time using a sub file script. What happened is that the .sub file attempted to run the simulation 24 times instead of parallelizing it over the 24 processors Here are the contents of run_1.sub file I tried to use to parallelize the simulation using qsub run_1.sub #PBS -S /bin/bash #PBS -N run_1 #PBS -l nodes=3:ppn=8 module load openmpi/gnu mpirun -np 24 /home/hassan/bin/bin/mdrun_mpi -deffnm run_1 -v run_1_update.txt exit $? What happens it that it outputs 24 run_1.log files, starting from #run_1.log1# all the way to #run_1.log23#...Has anyone faced this problem before? and If yes, any hints or solutions? I do appreciate any help in that domain Hassan From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 12/6/2010 6:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pressure fluctuations Hassan Shallal wrote: Dear Gromacs users, I have some concerns about the both the pressure fluctuations and averages I obtained during the equilibration phase. I have already read through several similar posts as well as the following link http://www.gromacs.org/Documentation/Terminology/Pressure. I understand the pressure is a macroscopic rather than instantaneous property and the average is what really matters. I also found out through similar posts that negative average pressure indicates the system tendency to contract. In the above link, it mentioned that pressure fluctuations should decrease significantly with increasing the system's size. In my cases, I have a fairly big systems (case_1 with *17393* water molecules and case_2 with *11946 *water molecules). However, the pressure still has huge fluctuations (around 500 bars) from the reference value (1 bar). Here are the average pressure and density values resulting from the equilibration phases of two cases, please notice the negative average pressure values in both cases... Case_1_pressure: Energy Average Err.Est. RMSD Tot-Drift --- Pressure *-2.48342* 0.92369.709 -4.89668 (bar) Case_1_density: Energy Average Err.Est. RMSD Tot-Drift --- Density 1022.89 0.38 3.82532.36724 (kg/m^3) Case_2_pressure: Energy Average Err.Est. RMSD Tot-Drift --- Pressure *-8.25259*2.6423.681 -12.1722 (bar) Case_2_density: Energy Average Err.Est. RMSD Tot-Drift --- Density 1034.11 0.372.499641.35551 (kg/m^3) So I have some questions to address my concerns: 1- each of the above systems has a protein molecule, NaCl to give 0.15 M system and solvent (water) molecules... Could that tendency to contract be an artifact of buffering the system with sodium and chloride ions? I suppose anything is possible, but given that these are fairly standard conditions for most simulations, I tend to doubt it. My own (similar) systems do not show this problem. 2- how to deal with the tendency of my system to contract? Should I change the number of water molecules in the system? or Is it possible to improve the average pressure of the above systems by increasing the time of equilibration from 100 ps to may be 500 ps or even 1 ns? 3- Is there a widely used range of average pressure (for ref_p = 1 bar) that indicates acceptable equilibration of the system prior to the production? To answer #2 and #3 simultaneously - equilibration is considered finished when your system stabilizes at the appropriate conditions (usually temperature and pressure). Your results indicate that your equilibrium is insufficient. 4- I can't understand how the system has a tendency to contract whereas the average density of the solvent is already slightly higher than it should be (1000 kg/m^3). The contraction causes the density to rise. Pressure and density are not independent; density is a result of pressure. I would like to ignore the pressure based judgement of the above equilibration given that the average density values are very close to the natural value (1000 kg/m^3) (by the way I am using tip3p water model with CHARMM27 ff) Any comment!! It is not guaranteed that simulation
[gmx-users] Re: trouble parallelizing a simulation over a cluster
On Dec 8, 2010, at 1:03 PM, Hassan Shallal wrote: Thanks a lot Justin for the very helpful answers concerning the pressure equilibration. Using Berendsen Barostat over 200 ps has lead to the correct average pressure... I have another issue to discuss with you and with the Gromacs mailing list members; I have been trying to run a simulation on a computer cluster for the first time using a sub file script. What happened is that the .sub file attempted to run the simulation 24 times instead of parallelizing it over the 24 processors Here are the contents of run_1.sub file I tried to use to parallelize the simulation using qsub run_1.sub #PBS -S /bin/bash #PBS -N run_1 #PBS -l nodes=3:ppn=8 module load openmpi/gnu mpirun -np 24 /home/hassan/bin/bin/mdrun_mpi -deffnm run_1 -v run_1_update.txt exit $? What happens it that it outputs 24 run_1.log files, starting from #run_1.log1# all the way to #run_1.log23#...Has anyone faced this problem before? and If yes, any hints or solutions? This typically happens when using a serial mdrun. You should check with ldd whether mdrun_mpi is linked to the correct mpi library. Carsten I do appreciate any help in that domain Hassan From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 12/6/2010 6:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pressure fluctuations Hassan Shallal wrote: Dear Gromacs users, I have some concerns about the both the pressure fluctuations and averages I obtained during the equilibration phase. I have already read through several similar posts as well as the following link http://www.gromacs.org/Documentation/Terminology/Pressure. I understand the pressure is a macroscopic rather than instantaneous property and the average is what really matters. I also found out through similar posts that negative average pressure indicates the system tendency to contract. In the above link, it mentioned that pressure fluctuations should decrease significantly with increasing the system's size. In my cases, I have a fairly big systems (case_1 with *17393* water molecules and case_2 with *11946 *water molecules). However, the pressure still has huge fluctuations (around 500 bars) from the reference value (1 bar). Here are the average pressure and density values resulting from the equilibration phases of two cases, please notice the negative average pressure values in both cases... Case_1_pressure: Energy Average Err.Est. RMSD Tot-Drift --- Pressure *-2.48342* 0.92369.709 -4.89668 (bar) Case_1_density: Energy Average Err.Est. RMSD Tot-Drift --- Density 1022.89 0.38 3.82532.36724 (kg/m^3) Case_2_pressure: Energy Average Err.Est. RMSD Tot-Drift --- Pressure *-8.25259*2.6423.681 -12.1722 (bar) Case_2_density: Energy Average Err.Est. RMSD Tot-Drift --- Density 1034.11 0.372.499641.35551 (kg/m^3) So I have some questions to address my concerns: 1- each of the above systems has a protein molecule, NaCl to give 0.15 M system and solvent (water) molecules... Could that tendency to contract be an artifact of buffering the system with sodium and chloride ions? I suppose anything is possible, but given that these are fairly standard conditions for most simulations, I tend to doubt it. My own (similar) systems do not show this problem. 2- how to deal with the tendency of my system to contract? Should I change the number of water molecules in the system? or Is it possible to improve the average pressure of the above systems by increasing the time of equilibration from 100 ps to may be 500 ps or even 1 ns? 3- Is there a widely used range of average pressure (for ref_p = 1 bar) that indicates acceptable equilibration of the system prior to the production? To answer #2 and #3 simultaneously - equilibration is considered finished when your system stabilizes at the appropriate conditions (usually temperature and pressure). Your results indicate that your equilibrium is insufficient. 4- I can't understand how the system has a tendency to contract whereas the average density of the solvent is already slightly higher than it should be (1000 kg/m^3). The contraction causes the density to rise. Pressure and density are not independent; density is a result of pressure. I would like
[gmx-users] -symm option
Dear all does somebody knows how -symm option from g_density command do the calculations? Or in other word what is the basic of -symm option? Thanks -- 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] Hard Spheres
Hi all! I am trying to add some hard spheres to my simulation. As far as i can tell from the manual Gromacs supports only LJ or Buckingham for non-bonded interaction. Is there a way to add hard spheres to lets say a simulation of Water molecules without interfering into the regular water-water interaction? Thanks a lot in advance, Sascha TU Dortmund Laboratory of Thermodynamics -- 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] How to construct user specified bond potential
Jia Haitao wrote: Manual section 4.2.13 maybe not enough. My potential functional shape is much more complex. I need at least two different force constants as C6 and C12 in LJ potential function in section 6.7.2. I use this for block copolymer system. There is only two types of monomer(e.g. A, B) and two types of bond potential(e.g.A-A, B-B ). If I can form two tables related to the two different bond potential respectively (e.g. table 1 for A-A and table 2 for B-B), the problem will be solved. Is it possible to be done in Gromacs? Yes. This is not terribly clear in the manual, so I will update it, but you can indeed supply, i.e. table_b0.xvg, table_b1.xvg, table_b2.xvg, etc as necessary. -Justin On Tue, Dec 7, 2010 at 11:14 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Jia Haitao wrote: Hello, everyone In gromacs user manual 6.7, they form non-bond potentials using table files, What should I do if I want to use a new *Bond* potential? The new bond potential combines two harmonic bond potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a standard harmonic potential. Besides, according user manual 5.7, there is 10 function types in table 5.5. How can I use the 8th and 9th type? Is there some examples? . All the information related to what you want to do is in the manual, section 4.2.13. Per the caption of Table 5.5, bond type 8 will be used to generate exclusions (when running grompp); presumably type 9 will not. Hopefully someone will correct me if I'm wrong here. -Justin -- */ Jia Haitao State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022, CHINA /* -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- */ Jia Haitao State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022, CHINA /* -- 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/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] How to construct user specified bond potential
I have construct two table files: table_b0.xvg for A-A bond, table_b1.xvg for B-B bond. and generated the bonds part of the topology file like this: [ bonds ] ; aiaj funct table_numberk 1 28 01.000 2 38 01.000 .. 55 56 8 11.000 56 57 8 21.000 .. as force constant k is a function, so I set k = 1.000 and combine it with f. Am I correct? Thank you very much. I really appreciate your help, Justin. -- * Jia Haitao State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022, CHINA * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_energy: Energy names magic number mismatch
Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type= bluegene # @ output = $(job_name).$(jobid).out # @ error = $(job_name).$(jobid).err # @ environment = COPY_ALL; # @ wall_clock_limit= 24:00:00 # @ notification= always # @ bg_size = 64 # @ queue .../mpirun -cwd $PWD -mode VN -np 256 -exe .../mdrun_bgp_d -args -deffnm nvt1 -dds 0.5 -cpi nvt1.cpt -append And it is running perfectly fine. I can analyze the data using g_energy etc. But if after the run is finished I increase the number of time steps and submit run again or resubmit it after a crash (killed manually or due to 24 hours wall clock limit), using the same script provided above, the run itself looks fine, at least .log file looks as it should but when I try to analyze .edr file with g_energy tool I obtain the following error message: --- Program g_energy_d, VERSION 4.5.1 Source code file: ../../../src/gmxlib/enxio.c, line: 409 Fatal error: Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I would really appreciate any hint on this subject. Many thanks in advance. Mikhail. -- 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] How to construct user specified bond potential
Jia Haitao wrote: I have construct two table files: table_b0.xvg for A-A bond, table_b1.xvg for B-B bond. and generated the bonds part of the topology file like this: [ bonds ] ; aiaj funct table_numberk 1 28 01.000 2 38 01.000 .. 55 56 8 11.000 56 57 8 21.000 .. as force constant k is a function, so I set k = 1.000 and combine it with f. Am I correct? Probably not. You've listed a table for n=2 but you don't actually use a table_b2.xvg, from what you've indicated. Doing your own tests will be substantially faster than waiting for an email reply. If you encounter a specific problem, post that. -Justin Thank you very much. I really appreciate your help, Justin. -- */ Jia Haitao State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022, CHINA /* -- 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/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] g_energy: Energy names magic number mismatch
Hi, There have been some issues with version 4.5.1 and energy files and continuation. But I don't recall them being this fatal. Anyhow, it would be better to upgrade to version 4.5.3, which contains several bug fixes. Berk From: mstu...@slb.com To: gmx-users@gromacs.org Date: Wed, 8 Dec 2010 13:50:21 + Subject: [gmx-users] g_energy: Energy names magic number mismatch Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh## @ account_no = xxx# @ job_name= NVT1 # @ job_type= bluegene # @ output = $(job_name).$(jobid).out # @ error = $(job_name).$(jobid).err # @ environment = COPY_ALL; # @ wall_clock_limit= 24:00:00# @ notification= always # @ bg_size = 64 # @ queue …/mpirun -cwd $PWD -mode VN -np 256 -exe …/mdrun_bgp_d -args -deffnm nvt1 -dds 0.5 -cpi nvt1.cpt -append And it is running perfectly fine. I can analyze the data using g_energy etc. But if after the run is finished I increase the number of time steps and submit run again or resubmit it after a crash (killed manually or due to 24 hours wall clock limit), using the same script provided above, the run itself looks fine, at least .log file looks as it should but when I try to analyze .edr file with g_energy tool I obtain the following error message: ---Program g_energy_d, VERSION 4.5.1Source code file: ../../../src/gmxlib/enxio.c, line: 409 Fatal error:Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors--- I would really appreciate any hint on this subject. Many thanks in advance.Mikhail. -- 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] g_energy: Energy names magic number mismatch
Mikhail Stukan wrote: Dear gromacs users, I am facing the following problem while running gromacs 4.5.1 at BlueGene/P supercomputer. The job is submitted by the following script file: #!/bin/sh # # @ account_no = xxx # @ job_name= NVT1 # @ job_type= bluegene # @ output = $(job_name).$(jobid).out # @ error = $(job_name).$(jobid).err # @ environment = COPY_ALL; # @ wall_clock_limit= 24:00:00 # @ notification= always # @ bg_size = 64 # @ queue …/mpirun -cwd $PWD -mode VN -np 256 -exe …/mdrun_bgp_d -args -deffnm nvt1 -dds 0.5 -cpi nvt1.cpt -append And it is running perfectly fine. I can analyze the data using g_energy etc. But if after the run is finished I increase the number of time steps and submit run again or resubmit it after a crash (killed manually or due to 24 hours wall clock limit), using the same script provided above, the run itself looks fine, at least .log file looks as it should but when I try to analyze .edr file with g_energy tool I obtain the following error message: --- Program g_energy_d, VERSION 4.5.1 Source code file: ../../../src/gmxlib/enxio.c, line: 409 Fatal error: Energy names magic number mismatch, this is not a GROMACS edr file For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I would really appreciate any hint on this subject. This was a Gromacs bug in versions 4.5.1 and 4.5.2. Please upgrade to version 4.5.3. http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x -Justin Many thanks in advance. Mikhail. -- 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/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] Umberella sampling
mohsen ramezanpour wrote: Dear All And Specially Dear Justin I read the toturial of Umbrella Sampling.It was very useful But there are afew question,of course about my work . 1-Is it necessary pulling one molecule along the line connecting their COMs? The pull code is based on COM distances, so in a basic sense, yes. But you don't necessarily have to have two entire molecules as your pull and reference groups; you can pull on a specific residue of one or the other, etc. Another type of PMF would be a dihedral rotation curve, so in a broad sense, PMF is not necessarily a linear calculation, but rather one that is carried out over a generic coordinate. 2-I have a protein-drug complex,it has oriented in a ordinary direction in 3D space How can I say Gromacs to pul drug along that line? See the pull_vec1 .mdp option. in the other words,are there any way to rotate system to an special direction? You can use editconf -rotate, but any arbitrary orientation can be utilized. -Justin thanks in advance for your guides. Mohsen -- 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/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] Can't build gromacs-4.5.3 with cmake
Hello gmx-users,
I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
have followed the INSTALL-GPU instructions along with the tips given
in this post: http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html
However, I am receiving the following error from cmake even without
the -DGMX_OPENMM=ON flag (and I have been making sure to rm
CMakeCache.txt and src/CMakeCache.txt):
u...@host:~/apps/gromacs-4.5.3$ cmake src/
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found assembler: /usr/bin/as
-- Loaded CMakeASM-ATTInformation - ASM-ATT support is still
experimental, please report issues
CMake Error at gmxlib/CMakeLists.txt:146 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at gmxlib/CMakeLists.txt:148 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmx.
CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at mdlib/CMakeLists.txt:13 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
md.
CMake Error at kernel/CMakeLists.txt:42 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at kernel/CMakeLists.txt:108 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxpreprocess.
CMake Error at kernel/CMakeLists.txt:109 (install):
install TARGETS given no RUNTIME DESTINATION for executable target mdrun.
CMake Error at kernel/CMakeLists.txt:110 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
grompp.
CMake Error at tools/CMakeLists.txt:36 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at tools/CMakeLists.txt:65 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxana.
CMake Error at tools/CMakeLists.txt:66 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
do_dssp.
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 2.8)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run cmake --help-policy CMP.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring incomplete, errors occurred!
Here are my environment variables:
PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/openmm/lib:
The variable that seems to be empty in CMakeLists.txt is
${LIB_INSTALL_DIR}. Does anyone know what that might be caused by?
Thank you,
Keith Callenberg
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Can't build gromacs-4.5.3 with cmake
What cmake version are you using?
On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg kmc...@pitt.edu wrote:
Hello gmx-users,
I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
have followed the INSTALL-GPU instructions along with the tips given
in this post:
http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html
However, I am receiving the following error from cmake even without
the -DGMX_OPENMM=ON flag (and I have been making sure to rm
CMakeCache.txt and src/CMakeCache.txt):
u...@host:~/apps/gromacs-4.5.3$ cmake src/
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found assembler: /usr/bin/as
-- Loaded CMakeASM-ATTInformation - ASM-ATT support is still
experimental, please report issues
CMake Error at gmxlib/CMakeLists.txt:146 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at gmxlib/CMakeLists.txt:148 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmx.
CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at mdlib/CMakeLists.txt:13 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
md.
CMake Error at kernel/CMakeLists.txt:42 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at kernel/CMakeLists.txt:108 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxpreprocess.
CMake Error at kernel/CMakeLists.txt:109 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
mdrun.
CMake Error at kernel/CMakeLists.txt:110 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
grompp.
CMake Error at tools/CMakeLists.txt:36 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at tools/CMakeLists.txt:65 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxana.
CMake Error at tools/CMakeLists.txt:66 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
do_dssp.
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 2.8)
should be added at the top of the file. The version specified may be
lower
if you wish to support older CMake versions for this project. For more
information run cmake --help-policy CMP.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring incomplete, errors occurred!
Here are my environment variables:
PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/openmm/lib:
The variable that seems to be empty in CMakeLists.txt is
${LIB_INSTALL_DIR}. Does anyone know what that might be caused by?
Thank you,
Keith Callenberg
--
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
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
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] COM
Dear All How can I know what is the vector which connect center of mass of two molecules(having their complex pdb file) ? Can I attain it by Gromacs or by Pymol? thanks in advance mohsen -- 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] COM
mohsen ramezanpour wrote: Dear All How can I know what is the vector which connect center of mass of two molecules(having their complex pdb file) ? Can I attain it by Gromacs or by Pymol? Use g_dist. -Justin thanks in advance mohsen -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_principal
Hi everyone, I'm trying to use g_principal for the first time. It gives 4 output files: axis1, axis2, axis3 moi.dat My question is: how can I know which axis correponds to the lowest eigenvalue? Nothing is mentioned in the manual. Thank you. Carla -- 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] Can't build gromacs-4.5.3 with cmake
I am running cmake version 2.8.0 on Ubuntu 10.04 64-bit with gcc 4.4.3.
~/apps/gromacs-4.5.3$ cmake -version
cmake version 2.8.0
Thanks,
Keith
What cmake version are you using?
On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg kmc112 at pitt.edu wrote:
Hello gmx-users,
I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
have followed the INSTALL-GPU instructions along with the tips given
in this post:
http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html
However, I am receiving the following error from cmake even without
the -DGMX_OPENMM=ON flag (and I have been making sure to rm
CMakeCache.txt and src/CMakeCache.txt):
user at host:~/apps/gromacs-4.5.3$ cmake src/
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found assembler: /usr/bin/as
-- Loaded CMakeASM-ATTInformation - ASM-ATT support is still
experimental, please report issues
CMake Error at gmxlib/CMakeLists.txt:146 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at gmxlib/CMakeLists.txt:148 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmx.
CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at mdlib/CMakeLists.txt:13 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
md.
CMake Error at kernel/CMakeLists.txt:42 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at kernel/CMakeLists.txt:108 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxpreprocess.
CMake Error at kernel/CMakeLists.txt:109 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
mdrun.
CMake Error at kernel/CMakeLists.txt:110 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
grompp.
CMake Error at tools/CMakeLists.txt:36 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at tools/CMakeLists.txt:65 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxana.
CMake Error at tools/CMakeLists.txt:66 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
do_dssp.
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 2.8)
should be added at the top of the file. The version specified may be
lower
if you wish to support older CMake versions for this project. For more
information run cmake --help-policy CMP.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring incomplete, errors occurred!
Here are my environment variables:
PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/openmm/lib:
The variable that seems to be empty in CMakeLists.txt is
${LIB_INSTALL_DIR}. Does anyone know what that might be caused by?
Thank you,
Keith Callenberg
--
gmx-users mailing listgmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Can't build gromacs-4.5.3 with cmake
Keith Callenberg wrote:
I am running cmake version 2.8.0 on Ubuntu 10.04 64-bit with gcc 4.4.3.
~/apps/gromacs-4.5.3$ cmake -version
cmake version 2.8.0
Does it make a difference if you build outside the source tree (as is
recommended)?
http://www.gromacs.org/Developer_Zone/Cmake#Using_CMake
-Justin
Thanks,
Keith
What cmake version are you using?
On Wed, Dec 8, 2010 at 9:49 AM, Keith Callenberg kmc112 at pitt.edu wrote:
Hello gmx-users,
I am trying to build gromacs-4.5.3 with GPU support with OpenMM. I
have followed the INSTALL-GPU instructions along with the tips given
in this post:
http://www.mail-archive.com/gmx-users@gromacs.org/msg34139.html
However, I am receiving the following error from cmake even without
the -DGMX_OPENMM=ON flag (and I have been making sure to rm
CMakeCache.txt and src/CMakeCache.txt):
user at host:~/apps/gromacs-4.5.3$ cmake src/
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found assembler: /usr/bin/as
-- Loaded CMakeASM-ATTInformation - ASM-ATT support is still
experimental, please report issues
CMake Error at gmxlib/CMakeLists.txt:146 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at gmxlib/CMakeLists.txt:148 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmx.
CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at mdlib/CMakeLists.txt:13 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
md.
CMake Error at kernel/CMakeLists.txt:42 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at kernel/CMakeLists.txt:108 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxpreprocess.
CMake Error at kernel/CMakeLists.txt:109 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
mdrun.
CMake Error at kernel/CMakeLists.txt:110 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
grompp.
CMake Error at tools/CMakeLists.txt:36 (set_target_properties):
set_target_properties called with incorrect number of arguments.
CMake Error at tools/CMakeLists.txt:65 (install):
install TARGETS given no ARCHIVE DESTINATION for static library target
gmxana.
CMake Error at tools/CMakeLists.txt:66 (install):
install TARGETS given no RUNTIME DESTINATION for executable target
do_dssp.
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 2.8)
should be added at the top of the file. The version specified may be
lower
if you wish to support older CMake versions for this project. For more
information run cmake --help-policy CMP.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring incomplete, errors occurred!
Here are my environment variables:
PATH=/usr/local/cuda/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/local/openmm/lib:
The variable that seems to be empty in CMakeLists.txt is
${LIB_INSTALL_DIR}. Does anyone know what that might be caused by?
Thank you,
Keith Callenberg
--
gmx-users mailing listgmx-users at 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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
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/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] Can't build gromacs-4.5.3 with cmake
Ah! Outside the source tree to me meant, outside src/. I see now that it means outside gromacs-4.5.3. It does indeed make a difference, now I can build. When I tried to compile with OpenMM I ran into an error that I was missing libxml-2.0. I had libxml2 installed, but I needed to install the headers using: sudo apt-get install libxml2-dev. When I tried to compile I got this error: $ make mdrun [ 0%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o CMake Error at CMakeFiles/gmx_gpu_utils_generated_memtestG80_core.cu.o.cmake:256 (message): Error generating file /home/keithc/apps/gromacs-4.5.3-gpu/src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o make[3]: *** [src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 This comes from some permissions issue from when I compiled the CUDA toolkit. I had just followed directions from a post on ubuntuforums, so I think others could potentially run into this issue as well. The (inelegant) workaround was to compile as sudo: sudo make mdrun (and) sudo make install-mdrun. Now it works. Thank you! Keith -- 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] Replacing charges of a residue, pdb2gmx -rtpo alternative?
On Tue, Dec 7, 2010 at 3:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 8/12/2010 4:07 AM, J. Nathan Scott wrote: Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am using) manual (pg 115) but does not seem to work, and yields the error Invalid command line argument: -rtpo when I try to use it I would basically like to have the OPLSAA aminoacids.rtp file in my working directory (which has some modified charges for the TRP residue) supersede the one in the Gromacs force field share directory. Is there a way to do this? So far I have resorted to copying the shared oplsaa.ff folder to my working directory and modifying the aminoacids.rtp file in that directory, and then selecting that directory to source my force field when I run pdb2gmx. This is the intended behaviour. Rather than modifying your installed database, or having to mess with the GMXLIB environment variable, you can copy the whole xx.ff directory into a local directory and have local modifications. pdb2gmx reports clearly on stdout which directory(s) it is (considering) using. This of course works, but I have noted a peculiar behavior using this method. No matter whether I select force field 1, which is OPLSAA from my working directory, or force field 15, which is OPLSAA from the share directory, my topology file ends up with charges in the working directory oplsaa.ff folder's aminoacids.rtp file. Even when I select that pdb2gmx should use the share version, it is clearly still using the force field folder in my working directory. I confirmed this by renaming the aminoacids.rtp in the working directory file to aminoacids.rtp.bak, which produced the error Could not find any files ending on '.rtp' in the force field directory 'oplsaa.ff' That sounds very weird. I'd suggest you start a new working directory, copy the oplsaa.ff over fresh, make the .rtp modifications and see if you can reproduce the issue. If so, please file a Bugzilla. Thanks for your reply Mark. I have confirmed this behavior many times now, and so I have filed a Bugzilla report as you suggested. I did find a quick fix: as long as the copy of the .ff directory in the working directory is named something different than the copy in share/top then pdb2gmx seems to differentiate between the two perfectly well, as confirmed by the charges in the topology files it is generating. It is only when they are named the same thing (oplsaa.ff, for instance) that the force field selection problem happens. Perhaps the programmers assumed users would be smart enough to rename the modified force field directory? ;) Best Wishes, -Nathan Can someone recommend a better method for what I am attempting to do? Also, is pdb2gmx's handling of force field directories appropriate? I had assumed that selecting the share version of a force field would force all the necessary files to be read from that share directory, but this is clearly not the case. It should be the case. Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- 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: correlation function
On 2010-12-08 20.51, samue...@ifi.unicamp.br wrote: Hello Dr. David gromacs calculate correlation function per atom with as velocity autocorrelation function and self - van hove correlation function in long time ( 0.1 microsenconds ) beacuse a work with supercooled liquids, of method is on the fly our post-processing file use FFT. If is on the fly you can send information of method and algorithm. I hope your help thank you very much Bye Samuel First, please ask further questions on the mailing list. GROMACS computes ACFs after compiling the data in one array. If you have memory problems the simplest solution is to either buy more memory or to split the calculation over molecules. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Regarding parameters of octane box in ffamber99sb - ildn
Hello all I have to create an octane box for studying effect of solvent hydrophobicity on enzyme activation. Anyone using octane parameterized file in amber? Please suggest me how to parameterize it or is there any tutorial for it. As i am a beginner, so plz explain in steps. Thanks a lot. Yuvraj On Mon, Dec 6, 2010 at 6:05 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Constraining two virtual sites (Mark Abraham) 2. Re: Help - LINCS WARNING: bonds that rotated more than30 degrees (Justin A. Lemkul) 3. RE: Constraining two virtual sites (Berk Hess) -- Forwarded message -- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Mon, 06 Dec 2010 22:31:55 +1100 Subject: Re: [gmx-users] Constraining two virtual sites On 6/12/2010 9:43 PM, Sebastian Fritsch wrote: Hi everybody, I have some trouble setting up topology for my, I admit, quite unusual system. I need to constrain the center of masses of two groups of atoms to a fixed 'bond' length. Since I have to do this for every molecule I cannot use the 'pull constraint' of the free energy code. Thus in my topology I defined a com vsite for each group and tried to apply a constraint between them. The atoms within each group are connected by harmonic springs forming a ring polymer (for those of you who know it: this is supposed to become the path integral representation in the end...) The topol.top for a single molecule test system looks like this: [ defaults ] ; nbfunc comb-rulegen-pairsfudgeLJfudgeQQ 1 1no1.01.0 [ atomtypes ] ;name masschargeptype C6 C12 ; sigma epsilon A 1.00800 0 A 0 0 B 1.00800 0 A 0 0 C 1.00800 0 A 0 0 VS 0.000 0 V 0 0 [ moleculetype ] ; molname nrexcl SOL0 [ atoms ] ; id at resnr resnm atnm cgnr charge 1 VS1 A V11 0 2 VS1 B V22 0 3 A 1 A A 3 0 4 B 1 A B 4 0 5 C 1 A C 5 0 6 A 1 B A 6 0 7 B 1 B B 7 0 8 C 1 B C 8 0 [ virtual_sitesN ] ; 1 2 3 4 5 2 2 6 7 8 [ bonds ] ; ai aj 3 4 1 0 1687 4 5 1 0 1687 5 3 1 0 1687 6 7 1 0 1687 7 8 1 0 1687 8 6 1 0 1687 [ constraints ] ; ai aj funct length_A 1 2 1 0.1633 [ system ] TEST [ molecules ] SOL 1 The conf.gro is setup such that the constraint is satisfied initially. When I run the simulation with LINCS the constraint seem to be not applied at all, the distance beetween the two vsites increases just as in free diffusion. With SHAKE the system explodes immediately (without error message, but every value is inf or nan). I am running the system with the sd integrator in (vers. 4.5.3) but also tried md and no thermostat, with no change in results. I appreciate any advice on this! Thanks, Sebastian I can't see anything that looks wrong. Make sure you inspect the output of grompp thoroughly for clues about how it's interpreting the .top file. You may like to use gmxcheck to compare the .tpr files produced under various permutations to see that things look like they're working correctly (remember atom numbers will start from zero in the output). Try putting the virtual site atoms after the real atoms in the ordering. Mark -- Forwarded message -- From: Justin A. Lemkul jalem...@vt.edu To: YUVRAJ UBOVEJA yuvraj.ubov...@students.iiit.ac.in, Gromacs Users' List gmx-users@gromacs.org Date: Mon, 06 Dec 2010 07:31:08 -0500 Subject: [gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than 30 degrees Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I am CC'ing the list and would ask that anything further be posted there. Before posting anything to the list, check the list archive. Your problem has been posted and answered literally thousands of times. Even better, the Gromacs site is full of helpful information, like the following: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin YUVRAJ UBOVEJA
Re: [gmx-users] Regarding parameters of octane box in ffamber99sb - ildn
YUVRAJ UBOVEJA wrote: Hello all I have to create an octane box for studying effect of solvent hydrophobicity on enzyme activation. Anyone using octane parameterized file in amber? Please suggest me how to parameterize it or is there any tutorial for it. As i am a beginner, so plz explain in steps. There is no substitute for reading the primary literature for your desired force field, and any previous publications upon which it is based. These papers should tell you the proper methods for geometry optimization, charge calculations, etc. Then, when you have a more thorough understanding of what approach you should take, you can post a more specific question about how to accomplish this task. Parameterization is often not a task well-suited to beginners. This should not discourage you from attempting your task, but please realize that the process of producing quality results is a long one, even for someone well-versed in exactly what is necessary. Proper derivation of parameters can take weeks, months, or years, depending on how complicated the process is. Take some time to learn how to use Gromacs for simple applications, understand the manual, understand your force field, then set out about your project. Also, in the future, please do not include the entire digest when you post. It confuses the archive. -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/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] anaeig
g_anaeig generated numbers of c-alpha or protein structures through -extr extreme.pdb. The bash shell show numbers of eigenvector structures starting from first to last frames are as follows eigenvector Minimum Maximum value time value time 1 4.88046714148.0 7.74721812501.0 2 1.63742113926.0 4.34406313110.0 3 -0.07439312567.0 2.74582614166.0 4 0.94024012618.0 5.18128314265.0 5 -2.76056614760.0 -0.10756412789.0 6 0.39418412627.0 2.69352014997.0 First column shows vectors, but what are the values in second column? Are they represents energy values in kJ/mol in second and fourth column? -- Pawan -- 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] Hard Spheres
On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de wrote: Hi all! I am trying to add some hard spheres to my simulation. As far as i can tell from the manual Gromacs supports only LJ or Buckingham for non-bonded interaction. Why cant you use LJ? By setting the attractive part equal to zero. Is there a way to add hard spheres to lets say a simulation of Water molecules without interfering into the regular water-water interaction? Thanks a lot in advance, Sascha TU Dortmund Laboratory of Thermodynamics -- 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] -symm option
try using to find out, its described on http://manual.gromacs.org/current/online/g_density.html On Wed, Dec 8, 2010 at 4:10 AM, Morteza Khabiri khab...@greentech.czwrote: Dear all does somebody knows how -symm option from g_density command do the calculations? Or in other word what is the basic of -symm option? Thanks -- 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: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko)
Try to run with mdrun -nt 1 1. Re: Re:6. QMMM, Segmentation fault (Olga Ivchenko) (Olga Ivchenko) 2. group temperatures and kinetic energies (Dmitri Dubov) 3. Re: group temperatures and kinetic energies (Dmitri Dubov) -- Message: 1 Date: Wed, 8 Dec 2010 10:19:00 +0100 From: Olga Ivchenkoolga.ivche...@gmail.com Subject: Re: [gmx-users] Re:6. QMMM, Segmentation fault (Olga Ivchenko) To: Discussion list for GROMACS usersgmx-users@gromacs.org Message-ID: aanlkti=ahmwhzimnrb96fz26cgxtfreiun=c2qaky...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Actually I am not sure that I can understand what is thread. But I can paste QMMM file here: -- 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] Hard Spheres
On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel sascha.hem...@bci.tu-dortmund.de wrote: Hi all! I am trying to add some hard spheres to my simulation. As far as i can tell from the manual Gromacs supports only LJ or Buckingham for non-bonded interaction. Why cant you use LJ? By setting the attractive part equal to zero. The LJ Equation is 4 * eps * ( (sig/r)**12 - (sig/r)**6). If I either set sigma or epsilon to zero the Potential will become zero for all r Is there a way to add hard spheres to lets say a simulation of Water molecules without interfering into the regular water-water interaction? Thanks a lot in advance, Sascha TU Dortmund Laboratory of Thermodynamics -- 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
