[gmx-users] Re.: genion doubt (manjula kasinathan)
Dear manjula kasinathan There aren't the warning parameter in gromacs, please remove the warning option in your mdp, if you need, add the flag -maxwarn in the grompp command, grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr -maxwarn 10 your simulation presents Lincs warnings, read the gromacs's errors page: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings good luck Jessé -- 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] Enc: 1-4 ineractions in double precision
Hi justin; I'm grateful for your help, but unfortunately I didn't solve the problem. I made a change in my mdp file. This is my mdout.mdp: == ; ;File 'mdout.mdp' was generated ;By user: jesse (1001) ;On host: slayer ;At date: Fri Dec 18 16:14:29 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 100 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 500 nstvout = 500 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.9 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 3.400 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale ; Groups to couple separately tc-grps = Protein Non-Protein ; Time constant (ps) and reference
[gmx-users] 1-4 ineractions in double precision
Dear Gromacs users; I have got a problem when performing molecular dynamics calculations in double precision with Gromacs Version 4.0.7. My system contains a protein with 482 residues, water molecules and Cl-ions. I have already carried out this same calculation in single precision with success. Below, I show my output and input files for the calculation in double precision. === starting mdrun 'Protein in water' 100 steps, 2000.0 ps. Warning: 1-4 interaction between 4412 and 4417 at distance inf which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 4365 and 4368 at distance inf which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 4649 and 4655 at distance inf which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation Warning: 1-4 interaction between 1336 and 1339 at distance inf which is larger than the 1-4 table size 2.400 nm This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 1199 and 1211 at distance inf which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Warning: 1-4 interaction between 525 and 529 at distance inf which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size rank 2 in job 7 slayer_37486 caused collective abort of all ranks exit status of rank 2: killed by signal 9 === My mdp file is: == title : ldtop1 cpp : /usr/bin/cpp ; the c processor integrator : md dt : 0.002 nsteps: 100 nstcomm:1 nstxout:500 nstvout:500 nstfout:0 nstlist:5 ns_type:grid rlist:0.9 coulombtype:PME rcoulomb:0.9 rvdw:1.4 table-extension:4.000 fourierspacing:0.12 fourier_nx:0 fourier_ny:0 fourier_nz:0 pme_order:14 ewald_rtol:1e-5 optimize_fft:yes constraint_algorithm:LINCS constraints:hbonds lincs_order :6 ; ; Berendsen temperature coupling ; Tcoupl : V-rescale tau_t : 0.1 0.1 0.1 tc-grps: protein SOL CL- ref_t : 300 300 300 ; ; Pressure Coupling ; Pcoupl : berendsen pcoupltype: isotropic tau_p : 0.5 compressibility : 4.5e-5 ref_p : 1.0 ; ; Generate velocity ; gen_vel: yes gen_temp : 300.0 gen_seed : 173529 === Any help would be appreciated, and if you require further information please let me know. Thanks in advance. Jesse da Nóbrega Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Including K+ in gromos96
Date: Mon, 6 Jul 2009 16:52:51 -0500 From: sadhna joshi sadhna.jo...@gmail.com Subject: [gmx-users] including K ion in gromos96 To: gmx-users@gromacs.org Message-ID: ffc8f9170907061452y4b5ea1e4jacfc4b81dfc12...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 hi, I am using gromacs 3.3.1 and ions.itp does not have K ion (in gromos96). I tried to include it by making K.itp and including in topology file. I get the following error.. Invalid order for directive atoms, file K.itp, line 1 I am not sure where I am wrong,,, thanks sadhna Hi sadhna, You must read the manual chapter five, after, you must see the ions.itp and ?nb.itp files and note if there are parameters for K ion. You must include the parameters for the ion K and for the Cl ions, if you try to create a file k.itp, follow the same steps but adding the mass of the ion. Good Luck Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Charge pertubation
Hi all, There are a gromacs's program for introducing a charge value in residue or make modifications in the topology file?? How analises the residue's charge of a protein? Thank you Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Thank you
Dear Justin; Thank you very much, your answers solved my questions, but ocurred new errors which will resolve to further. I go try new parameters create for PVC's atoms now. Thank you Jessé da Nóbrega Graduating in pharmacy from the Federal University of Paraíba - Brazil Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] building Topologies
Hi gmx-users, I have trying build topologies for PVC polymer in opls/aa forcefield. I read the chapter 5 and modified the files ffoplsaa.rtp, ffoplsaa.hdb, ffoplsaa-n.tdb, ffoplsaa-c.tdb, but not successful. Below, you can see the blocks that built. The parameters for the residue may seem confusing, but I am trying to understand how to build these blocks and then create new parameters for the residue. rtp file: [ VIN ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_001 0.5002 Cl opls_151-0.2002 H21 opls_153 0.1032 [ bonds ] C1 H11 C1 H12 C1 C2 C2 Cl C2 H21 C2 +C1 hdb file VIN 2 2 6 H1 C1 C2 +C1 1 6 H2 C2 C1 -C2 -c.tdb file: [ VIN ] [ replace ] C1 opls_13512.011 -0.18 [ add ] 34 H1 C1 C2 opls_140 1.008 0.06 [ delete ] H21 -n.tdb file: [ VIN ] [ replace ] C opls_15212.011 -0.006 [ add ] 2 4H C2 C1 opls_1531.00800 0.103 [ delete ] H21 By using the pdb2gmx following error occurs: Opening library file ffoplsaa.rtp Opening library file /usr/local/gromacs332/share/gromacs/top/aminoacids.dat Reading PVC_32_mon_1_cd_gromos.pdb... WARNING: all CONECT records are ignored Read 194 atoms Opening library file /usr/local/gromacs332/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 32 residues with 194 atoms chain #res #atoms 1 ' '32194 All occupancies are one Opening library file /usr/local/gromacs332/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file ffoplsaa.hdb Opening library file ffoplsaa-n.tdb --- Program pdb2gmx_mpi, VERSION 3.3.2 Source code file: h_db.c, line: 95 Fatal error: Error in hdb file ffoplsaa-n.tdb: Wrong number of control atoms (2 iso 3) on line: 2 4H C2 C1 Why this error occur? Excuse me my English, I am a beginner in the language. Thank you very much Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
