Re: [gmx-users] gromacs installation problem in ibm powerpc system
- Original Message - From: Sanku M msank...@yahoo.com Date: Monday, May 31, 2010 13:00 Subject: [gmx-users] gromacs installation problem in ibm powerpc system To: gmx-users@gromacs.org Hi, I am having a problem in a cluster which is IBM PowerPC 970MPs and running SUSE linux and it has IBM XL C Fortran compliers ( xlf, xlc ). I was trying to install gromacs 4 there using open-mpi which is already installed using ibm compilers. Here is my configure command: ./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ --enable-mpi --program-suffix=mod_4mpi CPPFLAGS=-I/N/soft/linux-sles9-ppc64/fftw3-64-single/include LDFLAGS=-L/N/soft/linux-sles9-ppc64/fftw3-64-single/lib/ --without-x CC=xlc F77=xlf CXX=xlc++ The configuration part went OK. But when I wrote make, it fails with following error: nb_kernel010_ppc_altivec.h, line 42.44: 1506-275 (S) Unexpected text p_nri encountered. Assuming you're trying to install GROMACS 4.0.5 (which would have been good to mention), it has a bunch of restrict keywords in these arguments. Bizarrely, these are not found in any other GROMACS version, nor in the git repository, so someone did something weird there. Anyway, you can get rid of them by installing GROMACS 4.0.7, which has a bunch of bug fixes anyway... Mark nb_kernel010_ppc_altivec.h, line 42.76: 1506-275 (S) Unexpected text iinr encountered. nb_kernel010_ppc_altivec.h, line 42.102: 1506-275 (S) Unexpected text jindex encountered. nb_kernel010_ppc_altivec.h, line 43.70: 1506-275 (S) Unexpected text jjnr encountered. nb_kernel010_ppc_altivec.h, line 43.98: 1506-275 (S) Unexpected text shift encountered. nb_kernel010_ppc_altivec.h, line 43.124: 1506-275 (S) Unexpected text shiftvec encountered. nb_kernel010_ppc_altivec.h, line 44.70: 1506-275 (S) Unexpected text fshift encountered. nb_kernel010_ppc_altivec.h, line 44.98: 1506-275 (S) Unexpected text gid encountered. nb_kernel010_ppc_altivec.h, line 44.124: 1506-275 (S) Unexpected text pos encountered. nb_kernel010_ppc_altivec.h, line 45.70: 1506-275 (S) Unexpected text faction encountered. nb_kernel010_ppc_altivec.h, line 45.98: 1506-275 (S) Unexpected text charge encountered. nb_kernel010_ppc_altivec.h, line 45.123: 1506-275 (S) Unexpected text p_facel encountered. nb_kernel010_ppc_altivec.h, line 46.69: 1506-275 (S) Unexpected text p_krf encountered. nb_kernel010_ppc_altivec.h, line 46.100: 1506-275 (S) Unexpected text p_crf encountered. nb_kernel010_ppc_altivec.h, line 46.130: 1506-275 (S) Unexpected text Vc encountered. nb_kernel010_ppc_altivec.h, line 47.70: 1506-275 (S) Unexpected text type encountered. nb_kernel010_ppc_altivec.h, line 47.96: 1506-275 (S) Unexpected text p_ntype encountered. nb_kernel010_ppc_altivec.h, line 47.126: 1506-275 (S) Unexpected text vdwparam encountered. nb_kernel010_ppc_altivec.h, line 48.70: 1506-275 (S) Unexpected text Vvdw encountered. nb_kernel010_ppc_altivec.h, line 48.97: 1506-275 (S) Unexpected text p_tabscale encountered. make[5]: *** [nb_kernel010_ppc_altivec.lo] Error 1 make[5]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib/nonbonded/nb_kernel_ppc_altivec' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib/nonbonded' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src' make: *** [all-recursive] Error 1 Not sure what it means. Any help to resolve the issue will be highly appreciated. Sanku | --- -- gmx-users mailing list 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. 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] water clusters MD
Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to solvate highly ordered heavy water clusters in box of light water. At the first step when I execute pdb2gmx -f watercluster.pdb I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? Thanks a lot Oleksandr -- 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] water clusters MD
- Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Monday, May 31, 2010 18:48 Subject: [gmx-users] water clusters MD To: gmx-users@gromacs.org Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to solvate highly ordered heavy water clusters in box of light water. At the first step when I execute pdb2gmx -f watercluster.pdb I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? You're using a tool for a different job. pdb2gmx builds a topology file, mostly by constructing a [moleculetype] from a polymer of repeating units. Your moleculetypes are trivial, and at least one is already present in an .itp file for use with #include. editconf and genbox make a box and fill it with generic solvent. It will be simplest to either write your .top by hand, or adapt an existing .top, depending what you mean by heavy water. Either way, you'll need some fluency with GROMACS workflows and file types, so do all the general tutorial material you can find. If you'd done so, you might have realised that pdb2gmx is not really the tool for the job. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] box volume and solvant density
Dear all, I am running simulations of pure water at various temperatures. My first step is an annealing from the previous temperature to the next one, using a NPT ensemble. Using the result of that, I run an NVT simulation. Where can I recover the box average box dimensions, volume and density of water in the NVT run ? Using g_density, I am surprised to find that the density is varying by several percent; shouldn't it remain constant ? Thanks in advance for your insights JP Grivet -- 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] box volume and solvant density
grivet wrote: Dear all, I am running simulations of pure water at various temperatures. My first step is an annealing from the previous temperature to the next one, using a NPT ensemble. Using the result of that, I run an NVT simulation. Where can I recover the box average box dimensions, volume and density of water in the NVT run ? Use g_energy. Using g_density, I am surprised to find that the density is varying by several percent; shouldn't it remain constant ? Is this under NPT? Constant and fixed are somewhat different. Constant implies conserved, fluctuating about an average value. Fixed implies that there is no variation, essentially an artificial condition. -Justin Thanks in advance for your insights JP Grivet -- 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] mpi-run2
Dear Justin, Let me tell the details: I have a PC with 4 CPU, Fedora 11 x86_64 is installed, The rpm files of Gromacs 4 are installed, now, I want to configure the gromacs to use all 4 CPUs, At the end of configuration process, it says that the FFTW could not be found! The fftw files are installed in /usr/lib64 The problem is that how I can define this path for configuration process! I would be pleased if you kindly help me by more paitiance of course! Thanks. Mahmoud -- 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] mpi-run2
On Mon, 2010-05-31 at 07:38 -0700, nanogroup wrote: Dear Justin, Let me tell the details: I have a PC with 4 CPU, Fedora 11 x86_64 is installed, The rpm files of Gromacs 4 are installed, now, I want to configure the gromacs to use all 4 CPUs, At the end of configuration process, it says that the FFTW could not be found! Uhh.. Just to be clear: you have installed GROMACS from rpms. Then why do you want to compile GROMACS...? Btw: did you use the Fedora RPMs or the ones from the GROMACS website? The ones on the website are really old. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: box volume and solvant density
Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit : Justin A. Lemkul wrote: grivet wrote: Dear all, I am running simulations of pure water at various temperatures. My first step is an annealing from the previous temperature to the next one, using a NPT ensemble. Using the result of that, I run an NVT simulation. Where can I recover the box average box dimensions, volume and density of water in the NVT run ? Use g_energy. Appaerently no; g_energy gives me a choice of 37 variables to print (energies, pressure tensor, virial, etc..) but not box dimensions, volume or density. Is this because I am using 4.0.5 ? I should also add that under an NVT ensemble, none of these values will have changed from whatever the initial conditions were. Only under the influence of pressure coupling does the density vary (since the box vectors fluctuate). Volume is constant by virtue of the fact that you're using NVT. -Justin Using g_density, I am surprised to find that the density is varying by several percent; shouldn't it remain constant ? Thanks in advance for your insights JP Grivet My mistake. g_density outputs *partial* densities, with a default number of slices = 50. Setting -sl 0 recovers a single normal density. -- 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] Re: box volume and solvant density
grivet wrote: Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit : Justin A. Lemkul wrote: grivet wrote: Dear all, I am running simulations of pure water at various temperatures. My first step is an annealing from the previous temperature to the next one, using a NPT ensemble. Using the result of that, I run an NVT simulation. Where can I recover the box average box dimensions, volume and density of water in the NVT run ? Use g_energy. Appaerently no; g_energy gives me a choice of 37 variables to print (energies, pressure tensor, virial, etc..) but not box dimensions, volume or density. Is this because I am using 4.0.5 ? No, it's probably because you're using an NVT ensemble. See the comment from my previous message. If the values can't change then they likely won't be written to the .edr file (since it's a waste of space). -Justin I should also add that under an NVT ensemble, none of these values will have changed from whatever the initial conditions were. Only under the influence of pressure coupling does the density vary (since the box vectors fluctuate). Volume is constant by virtue of the fact that you're using NVT. -Justin Using g_density, I am surprised to find that the density is varying by several percent; shouldn't it remain constant ? Thanks in advance for your insights JP Grivet My mistake. g_density outputs *partial* densities, with a default number of slices = 50. Setting -sl 0 recovers a single normal density. -- 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 -- 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] Re: box volume and solvant density
On 31.05.2010, at 17:37, grivet wrote: Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit : Justin A. Lemkul wrote: grivet wrote: Dear all, I am running simulations of pure water at various temperatures. My first step is an annealing from the previous temperature to the next one, using a NPT ensemble. Using the result of that, I run an NVT simulation. Where can I recover the box average box dimensions, volume and density of water in the NVT run ? Use g_energy. Appaerently no; g_energy gives me a choice of 37 variables to print (energies, pressure tensor, virial, etc..) but not box dimensions, volume or density. Is this because I am using 4.0.5 ? No this is because you are simulating NVT, so you know your box dimensions. /Flo I should also add that under an NVT ensemble, none of these values will have changed from whatever the initial conditions were. Only under the influence of pressure coupling does the density vary (since the box vectors fluctuate). Volume is constant by virtue of the fact that you're using NVT. -Justin Using g_density, I am surprised to find that the density is varying by several percent; shouldn't it remain constant ? Thanks in advance for your insights JP Grivet My mistake. g_density outputs *partial* densities, with a default number of slices = 50. Setting -sl 0 recovers a single normal density. -- 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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- 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 direction of Electric fields in GROMACS?
On 5/31/10 6:21 PM, zhongjin wrote: Dear users, What's about the direction of Electric fields in GROMACS? For example, E_z 1 0.01 5 means that the direction of Electric fields is along the +Z axis ? So K+ will move along the +Z axis ? E_z 1 -0.01 5 means that the direction of Electric fields is along the -Z axis ? So Cl- will move along the -Z axis ? Anybody knows the answer? Please tell me. Thanks a lot ! He Zhongjin 2010-6-1 I think this is correct. You might want to try this in an empty box with just 1 K+ and one CL- (in vacuum that is, no water). -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://xray.bmc.uu.se/~spoel -- 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] Simulation explodes (protein-ligand-protein)
Hi! We have a problem with a protein-ligand-protein simulation. It is a somewhat large system (approx. 360 amino acid residues with approx. 70 monosaccharides), that requires a larger box for proper simulation. We used exclusions (especifically for the problematic atoms) and restrictions (tested values of 5000, 2000, 1000 - for backbone and for monosaccharides), both combined and individually, and when they were kept for the entire simulation, it went just fine. But when these restrictions and exclusions were removed, the glycan portion, that isnt connected to any of the proteins explodes. Any suggestions? Thank you in advance, Hi, We used the gromos43a1 force fied, and the .mdp with minimization parameters with no restraints or exclusions were: title = Yo cpp = /lib/cpp define = -DFLEX constraints = all-bonds integrator = md tinit = dt = 0.0005 ; ps ! nsteps = 200 ; total 0-1000 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 optimize_fft= yes pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tc-grps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+ tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ref_t = 50 50 50 50 50 50 50 50 ; Energy monitoring energygrps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+ ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 100 K. gen_vel = yes gen_temp= 10.0 gen_seed= 173529 This .mdp file works fine without water, but when we include sol the simulation explodes, too. The tc-grps in this case are a glycoprotein (protein-1, gli_1, gli_2, gli_3, gli_4 and gli_5) and a secondary protein (protein-2). thank you again, Giovana Bergamini Faculdade de Farmácia Grupo de Bioinformatica Estrutural Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 Prédio 43431, sala 202 CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil tel.: +55 51 3308 7770 http://www.cbiot. ufrgs.br/ bioinfo Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul -- 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] Simulation explodes (protein-ligand-protein)
Giovana Bergamini wrote: Hi! We have a problem with a protein-ligand-protein simulation. It is a somewhat large system (approx. 360 amino acid residues with approx. 70 monosaccharides), that requires a larger box for proper simulation. We used exclusions (especifically for the problematic atoms) and restrictions (tested values of 5000, 2000, 1000 - for backbone and for monosaccharides), both combined and individually, and when they were kept for the entire simulation, it went just fine. But when these restrictions and exclusions were removed, the glycan portion, that isn’t connected to any of the proteins “explodes”. Any suggestions? Thank you in advance, Hi, We used the gromos43a1 force fied, and the .mdp with minimization parameters with no restraints or exclusions were: title = Yo cpp = /lib/cpp define = -DFLEX constraints = all-bonds integrator = md tinit = dt = 0.0005 ; ps ! nsteps = 200 ; total 0-1000 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 optimize_fft= yes pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tc-grps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+ tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ref_t = 50 50 50 50 50 50 50 50 ; Energy monitoring energygrps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+ ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 100 K. gen_vel = yes gen_temp= 10.0 gen_seed= 173529 This .mdp file works fine without water, but when we include sol the simulation explodes, too. The tc-grps in this case are a glycoprotein (protein-1, gli_1, gli_2, gli_3, gli_4 and gli_5) and a secondary protein (protein-2). Are each of these groups sufficiently large to justify their own temperature coupling group? I'd be especially concerned about coupling ions alone (presumably there are only a few CA+?) http://www.gromacs.org/Documentation/Terminology/Thermostats If you can identify that certain molecules are unstable, then I'd suspect as well that there might be problems with the topology. How did you generate it? How did you validate the parameters? Do simulations of the sugar moieties alone (using your topology) run stably? -Justin thank you again, Giovana Bergamini Faculdade de Farmácia Grupo de Bioinformatica Estrutural Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 Prédio 43431, sala 202 CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil tel.: +55 51 3308 7770 http://www.cbiot. ufrgs.br/ bioinfo Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul -- 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] add missing atoms
Hi again,Sorry, in REMARK 470 there is:REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2OG REMARK 470 GLN A 678CA C OCB CG CD OE1 NE2 REMARK 470 SER B 2OG REMARK 470 GLY B 679CA C O This means there are missing atoms. Is it possible to add these atoms from other residue what are SER and GLN and GLY?( Copy and Paste OG from other SER for example?) I think after EM these are fixed, it is true? Thank you Hi everyone, I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its. There's no automated GROMACS tool, and I haven't used any other particular tool for the task. For just one atom + hydrogen, you're probably fine to guess approximate coordinates and use EM to fix it. _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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] add missing atoms
you zou wrote: Hi again, Sorry, in REMARK 470 there is: REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2OG REMARK 470 GLN A 678CA CO nbs p; CB CG CD OE1 NE2 REMARK 470 SER B 2OG REMARK 470 GLY B 679CA CO This means there are missing atoms. Is it possible to add these atoms from other residue what are SER and GLN and GLY?( Copy and Paste OG from other SER for example?) I think after EM these are fixed, it is true? If you have several missing atoms you will have to use some external tool(s) to re-create these residues. Using cute tricks to build back one atom is easy enough, but re-creating a fragmented structure is much easier using tools designed for the task. -Justin Thank you Hi everyone, br I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its. There's no automated GROMACS tool, and I haven't used any other particular tool for the task. For just one atom + hydrogen, you're probably fine to guess approximate coordinates and use EM to fix it. Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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] QMMM cpmd
I've downloaded gromacs from the git repository. I type ./bootstrap and get loads of warnings like this configure.ac:414: warning: AC_CACHE_VAL(ac_m_cpu_7450, ...): suspicious cache-id, must contain _cv_ to be cached configure.ac:414: warning: AC_CACHE_VAL(ac_m_tune_970, ...): suspicious cache-id, must contain _cv_ to be cached Plus, when I type ./configure CFLAGS=-DGMX_QMMM_CPMD --with-qmmm-cpmd, configure runs fine except for this warning: configure: WARNING: unrecognized options: --with-qmmm-cpmd I figure that if ./configure does not recognize the cpmd option, there is no point in trying to compile gromacs with cpmd, I mean, the make command is not going to include cpmd, or is it? Some help on the matter would be appreciated. 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] vibrational spectra of glucose
Hello, I want to calculate the normal vibrational spectra of PF6 anion. After the energy minimization, I found that the structure has lost his symmetry. It does not have Oh symetry. I compared this structre with ab-initio which is not matching. I have pasted the input file for energy minimzation. WHy structure is loosing its symmetry or why its not giving proper local minima. Nilesh define = -DFLEXIBLE constraints = none integrator = L-BFGS nsteps = 5 nbfgscorr= 50 emtol= 0.0001 emstep = 0.0001 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist =10 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist= 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0 -- 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] water clusters MD
Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say I don't need it. Ok may be topology file can be written by hand, but what about gro file? --- On Mon, 5/31/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, May 31, 2010, 10:55 AM - Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Monday, May 31, 2010 18:48 Subject: [gmx-users] water clusters MD To: gmx-users@gromacs.org Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to solvate highly ordered heavy water clusters in box of light water. At the first step when I execute pdb2gmx -f watercluster.pdb I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? You're using a tool for a different job. pdb2gmx builds a topology file, mostly by constructing a [moleculetype] from a polymer of repeating units. Your moleculetypes are trivial, and at least one is already present in an .itp file for use with #include. editconf and genbox make a box and fill it with generic solvent. It will be simplest to either write your .top by hand, or adapt an existing .top, depending what you mean by heavy water. Either way, you'll need some fluency with GROMACS workflows and file types, so do all the general tutorial material you can find. If you'd done so, you might have realised that pdb2gmx is not really the tool for the job. Mark -- gmx-users mailing list 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. 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] “Fatal error in PMPI_Bcast: Ot her MPI error, …..” occurs when using the ‘particle decomposition’ option.
Hi, everyone of gmx-users, I met a problem when I use the ‘particle decomposition’ option in a NTP MD simulation of Engrailed Homeodomain (En) in CL- neutralized water box. It just crashed with an error “Fatal error in PMPI_Bcast: Other MPI error, error stack: …..”. However, I’ve tried the ‘domain decomposition’ and everything is ok! I use the Gromacs 4.05 and 4.07, the MPI lib is mpich2-1.2.1p1. The system box size is 5.386(nm)3. The MDP file list as below: title= En ;cpp = /lib/cpp ;include = -I../top define = integrator = md dt = 0.002 nsteps = 300 nstxout = 500 nstvout = 500 nstlog = 250 nstenergy= 250 nstxtcout = 500 comm-mode = Linear nstcomm = 1 ;xtc_grps = Protein energygrps = protein non-protein nstlist = 10 ns_type = grid pbc = xyz ;default xyz ;periodic_molecules = yes ;default no rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = v-rescale tc_grps = protein non-protein tau_t= 0.1 0.1 ref_t= 298 298 Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints = hbonds lincs_order = 10 When I conduct MD using “nohup mpiexec -np 2 mdrun_dmpi -s 11_Trun.tpr -g 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo 12_NTPstate.cpt ”, everything is OK. Since the system doesn’t support more than 2 processes under ‘domain decomposition’ option, it took me about 30 days to calculate a 6ns trajectory. Then I decide to use the ‘particle decomposition’ option. The command line is “nohup mpiexec -np 6 mdrun_dmpi -pd -s 11_Trun.tpr -g 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo 12_NTPstate.cpt ”. And I got the crash in the nohup file like below: Fatal error in PMPI_Bcast: Other MPI error, error stack: PMPI_Bcast(1302)..: MPI_Bcast(buf=0x8fedeb0, count=60720, MPI_BYTE, root=0, MPI_COMM_WORLD) failed MPIR_Bcast(998)...: MPIR_Bcast_scatter_ring_allgather(842): MPIR_Bcast_binomial(187)..: MPIC_Send(41).: MPIC_Wait(513): MPIDI_CH3I_Progress(150)..: MPID_nem_mpich2_blocking_recv(948): MPID_nem_tcp_connpoll(1720)...: state_commrdy_handler(1561)...: MPID_nem_tcp_send_queued(127).: writev to socket failed - Bad address rank 0 in job 25 cluster.cn_52655 caused collective abort of all ranks exit status of rank 0: killed by signal 9 And the ends of the log file list as below: …….. …….. …….. …….. bQMMM= FALSE QMconstraints= 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 I’ve search the gmx-users mail list and tried to adjust the md parameters, and no solution was found. The mpiexec -np x option doesn't work except when x=1. I did found that when the whole En protein is constrained using position restraints (define = -DPOSRES), the ‘particle decomposition’ option works. However this is not the kind of MD I want to conduct. Could anyone help me about this problem? And I also want to know how can I accelerate this kind of MD (long time simulation of small system) using Gromacs? Thinks a lot! (Further information about the simulated system: The system has one En protein (54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- used to neutralize the system. The system has been minimized first. A 20ps MD is also performed for the waters and ions before EM.) -- 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] water clusters MD
- Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Tuesday, June 1, 2010 11:39 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say You need neither file for editconf and genbox. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. You can use your existing correctly-formatted .pdb file. If you already have a .top for the original structure, genbox will update it suitably with the new waters. Mark I don't need it. Ok may be topology file can be written by hand, but what about gro file? --- On Mon, 5/31/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, May 31, 2010, 10:55 AM - Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Monday, May 31, 2010 18:48 Subject: [gmx-users] water clusters MD To: gmx-users@gromacs.org Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to solvate highly ordered heavy water clusters in box of light water. At the first step when I execute pdb2gmx -f watercluster.pdb I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? You're using a tool for a different job. pdb2gmx builds a topology file, mostly by constructing a [moleculetype] from a polymer of repeating units. Your moleculetypes are trivial, and at least one is already present in an .itp file for use with #include. editconf and genbox make a box and fill it with generic solvent. It will be simplest to either write your .top by hand, or adapt an existing .top, depending what you mean by heavy water. Either way, you'll need some fluency with GROMACS workflows and file types, so do all the general tutorial material you can find. If you'd done so, you might have realised that pdb2gmx is not really the tool for the job. Mark -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. 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] vibrational spectra of glucose
- Original Message - From: Nilesh Dhumal ndhu...@andrew.cmu.edu Date: Tuesday, June 1, 2010 10:37 Subject: [gmx-users] vibrational spectra of glucose To: gmx-users@gromacs.org Hello, I want to calculate the normal vibrational spectra of PF6 anion. After the energy minimization, I found that the structure has lost his symmetry. It does not have Oh symetry. I compared this That's normal. QM codes go to great lengths to recognize symmetry and use it because it makes the calculation quicker. MD codes don't bother, because they don't get used for systems with such high symmetry. structre with ab-initio which is not matching. I have pasted the input file for energy minimzation. WHy structure is loosing its symmetry or why its not giving proper local minima. It'll lose symmetry if it didn't have it to start with (so you'll need the axes to line up with F-P-F vectors), or if the force field is assymetric. I don't know of any force field that would claim to support parameters for PF6 anion, but presumably you've done your homework there. If so, the documentation there should mention how they ran it. This looks like a much easier problem for a QM code to solve - B3LYP/6-31G* is probably better than any MM parameterization, and with high symmetry, maybe quicker too! Mark define = -DFLEXIBLE constraints = none integrator = L-BFGS nsteps = 5 nbfgscorr = 50 emtol = 0.0001 emstep = 0.0001 gen_vel = yes gen- temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist =10 ; ns algorithm (simple or grid) ns- type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist = 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb- switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field ; Method for doing Van der Waals vdw- type = Cut-off ; cut-off lengths rvdw- switch = 0 rvdw = 0 -- gmx-users mailing list 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. 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] “Fatal error in PMPI_ Bcast: Other MPI error, …..” occurs when u sing the ‘particle decomposition’ option.
- Original Message - From: xho...@sohu.com Date: Tuesday, June 1, 2010 11:53 Subject: [gmx-users] “Fatal error in PMPI_Bcast: Other MPI error, …..” occurs when using the ‘particle decomposition’ option. To: gmx-users gmx-users@gromacs.org Hi, everyone of gmx-users, I met a problem when I use the ‘particle decomposition’ option in a NTP MD simulation of Engrailed Homeodomain (En) in CL- neutralized water box. It just crashed with an error “Fatal error in PMPI_Bcast: Other MPI error, error stack: …..”. However, I’ve tried the ‘domain decomposition’ and everything is ok! I use the Gromacs 4.05 and 4.07, the MPI lib is mpich2- 1.2.1p1. The system box size is 5.386(nm)3. The MDP file list as below: title = En ;cpp = /lib/cpp ;include = -I../top define = integrator = md dt = 0.002 nsteps = 300 nstxout = 500 nstvout = 500 nstlog = 250 nstenergy = 250 nstxtcout = 500 comm- mode = Linear nstcomm = 1 ;xtc_grps = Protein energygrps = protein non-protein nstlist = 10 ns_type = grid pbc = xyz;default xyz ;periodic_molecules = yes ;default no rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = v-rescale tc_grps = protein non-protein tau_t = 0.1 0.1 ref_t = 298 298 Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints = hbonds lincs_order = 10 When I conduct MD using “nohup mpiexec -np 2 mdrun_dmpi -s 11_Trun.tpr -g 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo 12_NTPstate.cpt ”, everything is OK. Since the system doesn’t support more than 2 processes under ‘domain decomposition’ option, it took me about 30 days to calculate a 6ns trajectory. Then I decide to use the ‘particle Why no more than 2? What GROMACS version? Why are you using double precision with temperature coupling? MPICH has known issues. Use OpenMPI. decomposition’ option. The command line is “nohup mpiexec -np 6 mdrun_dmpi -pd -s 11_Trun.tpr -g 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo 12_NTPstate.cpt ”. And I got the crash in the nohup file like below: Fatal error in PMPI_Bcast: Other MPI error, error stack: PMPI_Bcast(1302)..: MPI_Bcast(buf=0x8fedeb0, count=60720, MPI_BYTE, root=0, MPI_COMM_WORLD) failed MPIR_Bcast(998)...: MPIR_Bcast_scatter_ring_allgather(842): MPIR_Bcast_binomial(187)..: MPIC_Send(41).: MPIC_Wait(513): MPIDI_CH3I_Progress(150)..: MPID_nem_mpich2_blocking_recv(948): MPID_nem_tcp_connpoll(1720)...: state_commrdy_handler(1561)...: MPID_nem_tcp_send_queued(127).: writev to socket failed - Bad address rank 0 in job 25 cluster.cn_52655 caused collective abort of all ranks exit status of rank 0: killed by signal 9 And the ends of the log file list as below: …….. …….. …….. …….. bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 I’ve search the gmx-users mail list and tried to adjust the md parameters, and no solution was found. The mpiexec -np x option doesn't work except when x=1. I did found that when the whole En protein is constrained using position restraints (define = -DPOSRES), the ‘particle decomposition’ option works. However this is not the kind of MD I want to conduct. Could anyone help me about this problem? And I also want to know how can I accelerate this kind of MD (long time simulation of small system) using Gromacs? Thinks a lot! (Further information about the simulated system: The system has one En protein (54 residues, 629 atoms), total 4848 spce waters, and 7
Re: [gmx-users] water clusters MD
It would be helpful if you could be more specific. For example, the standard procedure described in tutorial: pdb2gmx -f input.pdb edit conf -f conf.gro d 0.5 -o newbox.gro genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb Now, could you please illustrate how would you do this for trivial non-protein molecules? --- On Tue, 6/1/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, June 1, 2010, 4:16 AM - Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Tuesday, June 1, 2010 11:39 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say You need neither file for editconf and genbox. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. You can use your existing correctly-formatted .pdb file. If you already have a .top for the original structure, genbox will update it suitably with the new waters. Mark I don't need it. Ok may be topology file can be written by hand, but what about gro file? --- On Mon, 5/31/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, May 31, 2010, 10:55 AM - Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Monday, May 31, 2010 18:48 Subject: [gmx-users] water clusters MD To: gmx-users@gromacs.org Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to solvate highly ordered heavy water clusters in box of light water. At the first step when I execute pdb2gmx -f watercluster.pdb I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? You're using a tool for a different job. pdb2gmx builds a topology file, mostly by constructing a [moleculetype] from a polymer of repeating units. Your moleculetypes are trivial, and at least one is already present in an .itp file for use with #include. editconf and genbox make a box and fill it with generic solvent. It will be simplest to either write your .top by hand, or adapt an existing .top, depending what you mean by heavy water. Either way, you'll need some fluency with GROMACS workflows and file types, so do all the general tutorial material you can find. If you'd done so, you might have realised that pdb2gmx is not really the tool for the job. Mark -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. 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] water clusters MD
- Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Tuesday, June 1, 2010 12:43 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org It would be helpful if you could be more specific. For example, the standard procedure described in tutorial: pdb2gmx -f input.pdb edit conf -f conf.gro d 0.5 -o newbox.gro genbox -cp newbox.gro -cs spc2165.gro -p topol.top -o solvated.pdb Now, could you please illustrate how would you do this for trivial non-protein molecules? editconf -d 0.5 -f pentamer.pdb -o newbox.gro genbox -cp newbox.gro -cs -o solvated.gro You can get some more information with editconf -h and genbox -h. Mark --- On Tue, 6/1/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, June 1, 2010, 4:16 AM - Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Tuesday, June 1, 2010 11:39 Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx-users@gromacs.org Look, in order to use editconf and gen box one need first to have gro and top files, which are generated by pdb2gmx. You say You need neither file for editconf and genbox. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. You can use your existing correctly-formatted .pdb file. If you already have a .top for the original structure, genbox will update it suitably with the new waters. Mark I don't need it. Ok may be topology file can be written by hand, but what about gro file? --- On Mon, 5/31/10, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] water clusters MD To: Discussion list for GROMACS users gmx- us...@gromacs.org Date: Monday, May 31, 2010, 10:55 AM - Original Message - From: Oleksandr nablaobl...@yahoo.com Date: Monday, May 31, 2010 18:48 Subject: [gmx-users] water clusters MD To: gmx-users@gromacs.org Hi, I'm new user of Gromacs. There are plenty examples how to do solvation study of various proteins. But I'd like to solvate highly ordered heavy water clusters in box of light water. At the first step when I execute pdb2gmx -f watercluster.pdb I get an error no matter which model is chosen: --- Fatal error: Atom H in residue HOH 4 not found in rtp entry with 3 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or choose a different protonation state. Option -ignh will ignore all hydrogens in the input. --- Can anybody help me how to solve this problem? You're using a tool for a different job. pdb2gmx builds a topology file, mostly by constructing a [moleculetype] from a polymer of repeating units. Your moleculetypes are trivial, and at least one is already present in an .itp file for use with #include. editconf and genbox make a box and fill it with generic solvent. It will be simplest to either write your .top by hand, or adapt an existing .top, depending what you mean by heavy water. Either way, you'll need some fluency with GROMACS workflows and file types, so do all the general tutorial material you can find. If you'd done so, you might have realised that pdb2gmx is not really the tool for the job. Mark -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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
Re: [gmx-users] Constraint causing system to explode
Chris, As you suggested, I ran it on one node, and it still blew up, so it appears to be some oddity with the constraint that I am imposing. When I look at the dgdl.xvg file from the run, there appear to be a number of transient spikes that are a couple orders of magnitude larger than the typical variation during the run, and I am getting errors on an angle changing by more than 30 degrees as a LINCS warning during those short spikes. The final system blow-up starts with the same situtation, which degenerates into a full blow system explosion, with bond lengths going to crzy high values. So my question boils down to this: What is it about a type 2 constraint that will generate these ridiculously large forces on relatively rare occasions? Or perhaps, what error am I making in setting up the simulation that would cause only the constrained system to manifest this behavior? Warren Gallin On 2010-05-27, at 11:22 AM, chris.ne...@utoronto.ca wrote: Dear Warren: I don't have your answer, but I'll point out that when you ask: Is it possible that this is a problem that arises because of domain decomposition over multiple nodes that you are probably the person in the best position to address this. 300ps should not take too long to simulate so why not try it on a single node and also on multiple nodes with mdrun -pd and report back? Somebody may have your answer, but the system blowing up question is so common that it is probably faster for you to rule out some things first. Chris. -- original message -- I am looking at the the free energy profile of end-to end distances of various peptides, but I am consistently getting a system blow-up when running simulations with that distance constrained by a type 2 constraint. I run a simulation of the unconstrained peptide in a box of tip4p water, Na+ and Cl- ions, and it runs with no problem. Then I grab a frame of that simulation in which the end-to-end distance is 0.8 nm (full frame including water) as a .gro file. Then I add a type 2 constraint between the N-terminal nitrogen atom and the C-terminal carboxyl carbon, create a new .tpr file using the revised topology and the already equilibrated frame as starting files and a .mdp file that now has the free_energy set to on, and then launch mdrun. About 189 ps into the simulation I start getting warnings as follows, ultimately leading to blow-up and the run failing (fragment of error file output shown at end of message). I am obviously missing something about how the constraint is handled. Is it possible that this is a problem that arises because of domain decomposition over multiple nodes, ir is there something more basic that needs to be dealt with when imposing a type 2 constraint? Warren Gallin Step 94636, time 189.272 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.041028, max 0.161215 (between atoms 217 and 219) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 94637, time 189.274 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.018884, max 0.100333 (between atoms 217 and 218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length SNIP -- 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] Constraint causing system to explode
- Original Message - From: Warren Gallin wgal...@ualberta.ca Date: Tuesday, June 1, 2010 13:38 Subject: Re: [gmx-users] Constraint causing system to explode To: Discussion list for GROMACS users gmx-users@gromacs.org Chris, As you suggested, I ran it on one node, and it still blew up, so it appears to be some oddity with the constraint that I am imposing. Does it happen with a distance restraint, instead? (Is that a better physical model?) Is there any possible correlation with one atom crossing a PBC boundary, such that a buggy implementation would then be horribly broken on the next step? Mark When I look at the dgdl.xvg file from the run, there appear to be a number of transient spikes that are a couple orders of magnitude larger than the typical variation during the run, and I am getting errors on an angle changing by more than 30 degrees as a LINCS warning during those short spikes. The final system blow-up starts with the same situtation, which degenerates into a full blow system explosion, with bond lengths going to crzy high values. So my question boils down to this: What is it about a type 2 constraint that will generate these ridiculously large forces on relatively rare occasions? Or perhaps, what error am I making in setting up the simulation that would cause only the constrained system to manifest this behavior? Warren Gallin On 2010-05-27, at 11:22 AM, chris.ne...@utoronto.ca wrote: Dear Warren: I don't have your answer, but I'll point out that when you ask: Is it possible that this is a problem that arises because of domain decomposition over multiple nodes that you are probably the person in the best position to address this. 300ps should not take too long to simulate so why not try it on a single node and also on multiple nodes with mdrun -pd and report back? Somebody may have your answer, but the system blowing up question is so common that it is probably faster for you to rule out some things first. Chris. -- original message -- I am looking at the the free energy profile of end-to end distances of various peptides, but I am consistently getting a system blow-up when running simulations with that distance constrained by a type 2 constraint. I run a simulation of the unconstrained peptide in a box of tip4p water, Na+ and Cl- ions, and it runs with no problem. Then I grab a frame of that simulation in which the end- to-end distance is 0.8 nm (full frame including water) as a .gro file. Then I add a type 2 constraint between the N- terminal nitrogen atom and the C-terminal carboxyl carbon, create a new .tpr file using the revised topology and the already equilibrated frame as starting files and a .mdp file that now has the free_energy set to on, and then launch mdrun. About 189 ps into the simulation I start getting warnings as follows, ultimately leading to blow-up and the run failing (fragment of error file output shown at end of message). I am obviously missing something about how the constraint is handled. Is it possible that this is a problem that arises because of domain decomposition over multiple nodes, ir is there something more basic that needs to be dealt with when imposing a type 2 constraint? Warren Gallin Step 94636, time 189.272 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.041028, max 0.161215 (between atoms 217 and 219) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 94637, time 189.274 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.018884, max 0.100333 (between atoms 217 and 218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length SNIP -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list 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. 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
[gmx-users] Re: gmx-users Digest, Vol 74, Issue 2
On Mon, May 31, 2010 at 10:17 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: add missing atoms (Justin A. Lemkul) 2. QMMM cpmd (Stefan Hoorman) 3. vibrational spectra of glucose (Nilesh Dhumal) 4. Re: water clusters MD (Oleksandr) 5. ?Fatal error in PMPI_Bcast: Other MPI error, ?..? occurs when using the ?particle decomposition? option. (xho...@sohu.com) 6. Re: water clusters MD (Mark Abraham) -- Message: 1 Date: Mon, 31 May 2010 19:48:43 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] add missing atoms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4c044adb.1000...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed hi you can add the missing residues in the whatif server. Manjula kasinathan. you zou wrote: Hi again, Sorry, in REMARK 470 there is: REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2OG REMARK 470 GLN A 678CA CO nbs p; CB CG CD OE1 NE2 REMARK 470 SER B 2OG REMARK 470 GLY B 679CA CO This means there are missing atoms. Is it possible to add these atoms from other residue what are SER and GLN and GLY?( Copy and Paste OG from other SER for example?) I think after EM these are fixed, it is true? If you have several missing atoms you will have to use some external tool(s) to re-create these residues. Using cute tricks to build back one atom is easy enough, but re-creating a fragmented structure is much easier using tools designed for the task. -Justin Thank you Hi everyone, br I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its. There's no automated GROMACS tool, and I haven't used any other particular tool for the task. For just one atom + hydrogen, you're probably fine to guess approximate coordinates and use EM to fix it. Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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 -- Message: 2 Date: Mon, 31 May 2010 20:49:25 -0300 From: Stefan Hoorman stefh...@gmail.com Subject: [gmx-users] QMMM cpmd To: gmx-users@gromacs.org Message-ID: aanlktin4ubtqxd0lqpbmlzw4nqod8-bkct7xx07e7...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 I've downloaded gromacs from the git repository. I type ./bootstrap and get loads of warnings like this configure.ac:414: warning: AC_CACHE_VAL(ac_m_cpu_7450, ...): suspicious cache-id, must contain _cv_ to be cached configure.ac:414: warning: AC_CACHE_VAL(ac_m_tune_970, ...): suspicious cache-id, must contain _cv_ to be cached Plus, when I type ./configure CFLAGS=-DGMX_QMMM_CPMD --with-qmmm-cpmd, configure runs fine except for this warning: configure: WARNING: unrecognized options: --with-qmmm-cpmd I figure that if ./configure does not recognize the cpmd option, there is no point in trying to compile gromacs with cpmd, I mean, the make command is not going to include cpmd, or is it? Some help on the matter would be appreciated. Thank you -- Message: 3 Date: Mon, 31 May 2010 20:36:09 -0400 From: Nilesh Dhumal ndhu...@andrew.cmu.edu Subject: [gmx-users] vibrational spectra of glucose To: gmx-users@gromacs.org Message-ID: 930ba257ed1041cec9cc7a20f96fb6cf.squir...@webmail.andrew.cmu.edu Content-Type: text/plain;charset=iso-8859-1 Hello, I want to calculate the normal vibrational spectra of PF6
[gmx-users] add missing atom(s)
Hi,Which tool(s) is/are useful? I don't have any idea for this problem.Thank you you zou wrote: Hi again, Sorry, in REMARK 470 there is: REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 2 OG REMARK 470 GLN A 678 CA C O nbs p; CB CG CD OE1 NE2 REMARK 470 SER B 2 OG REMARK 470 GLY B 679 CA C O This means there are missing atoms. Is it possible to add these atoms from other residue what are SER and GLN and GLY?( Copy and Paste OG from other SER for example?) I think after EM these are fixed, it is true? If you have several missing atoms you will have to use some external tool(s) to re-create these residues. Using cute tricks to build back one atom is easy enough, but re-creating a fragmented structure is much easier using tools designed for the task. -Justin _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969-- 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
