[gmx-users] FeS cluster
Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the protein .top file later as done in the case of drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial for the Fe4S4 cluster? With regards Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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
Re: [gmx-users] FeS cluster
subarna thakur wrote: Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the protein .top file later as done in the case of drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial for the Fe4S4 cluster? Yes and no. Even if you are able to obtain suitable parameters (which will be difficult at best), if there are bonded interactions to the cluster, then you will have to make a composite topology - i.e. a single [ moleculetype ]. Depending on the geometry and sequence order of your two chains, that might be painful too. Frankly, this project would be a very poor one for a first effort at MD. Get some experience with GROMACS doing something more straightforward, learning to walk, before trying to run juggling razors. 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] PLUMED release 1.1.0 available
The PLUMED Developers Team is proud to announce that the NEW version of PLUMED 1.1.0 is available at http://merlino.mi.infn.it/plumed PLUMED is a plugin for free-energy calculations in molecular systems that can be interfaced, through a simple patch procedure, with some of the most popular classical molecular dynamics codes. With PLUMED, the user can perform several type of calculations: - Metadynamics with a large variety of order parameters; - Combined parallel tempering and metadynamics; - Bias-exchange metadynamics; - Umbrella sampling; - Steered MD. In this NEW release: - Added support to ACEMD 1.1, NAMD 2.7b1, AMBER 10, DL POLY 2.20 and GROMACS 4.0.5. - PLUMED is now compatible with the domain-decomposition parallelization of GROMACS4 - The bias can be interpolated using cubic splines on a grid - Sum over hills is parallelized on GROMACS and DL POLY - More flexibility in the application of PBC to collective variable - Redesigned parallel tempering-metadynamics code - Redesigned parser and patching system, with more error checking - New collective variables: Electrostatic potential felt by a atom or group of atoms, Puckering variables (thanks to Marcello Sega). PLUMED is free software. You can redistribute it and/or modify it under the terms of the GNU Lesser General Public License. For more info, please refer to the PLUMED website. The PLUMED Developers Team___ 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] Position-restraint
Dear gmx-users, I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the following message: Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1108 Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I sent an email about this yesterday, but the advice was not applicable because of the set-up of my topology file. previous advice: ** Position restraints sections must be placed within the same [ moleculetype ] definition. So, you can't include all of the position restraint information in one file, since that file is part of the Protein [ moleculetype ] definition. The ligand should be placed in its own posre.itp file and included in the topology. These lines must be placed *outside* of the [ moleculetype ] directive of any other molecule(s) in the system. For consistency, whenever I have ligands, I place them immediately after the protein [ moleculetype ] and water topology, i.e.: #ifdef POSRES #include posre.itp #endif #include ligand.itp #ifdef POSRES_LIGAND #include ligand_posre.itp #endif #include spc.itp (etc). That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the ligand section begins with #include ligand.itp, ends with the POSRES_LIGAND section, and then the topology reads the water topology, etc. * This is the structure of my main topology file: ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include topol_A.itp #include topol_B.itp #include topol_C.itp #include topol_D.itp ; Include lipid topology #include popc_Stockner.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 Protein_C 1 Protein_D 1 POPC 288 SOL 33722 NA+ 28 *** At the end of the lipid topology file popc_Stockner.itp, I have placed the #include for the lipid position restraint file posre_lipid.itp. I tried moving the #include for the lipid position restraint into the main topology file, directly after the include lipid topology line, but this gives me the same error. Do you have any suggestions of where exactly to put the #include for the lipid position restraint? Thank you very much Dear gmx-users,I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the following message: Program grompp, VERSION 3.3Source code file: toppush.c, line: 1108Fatal error:[ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I sent an email about this yesterday, but the advice was not applicable because of the set-up of my topology file.previous advice: **Position restraints sections must be placed within the same [ moleculetype ] definition. So, you cant include all of the position restraint information in one file, since that file is part of the Protein [ moleculetype ] definition. The ligand should be placed in its own posre.itp file and included in the topology. These lines must be placed *outside* of the [ moleculetype ] directive of any other molecule(s) in the system. For consistency, whenever I have ligands, I place them immediately after the protein [ moleculetype ] and water topology, i.e.: #ifdef POSRES#include posre.itp#endif#include ligand.itp#ifdef POSRES_LIGAND#include ligand_posre.itp#endif#include spc.itp (etc).That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the ligand section begins with #include ligand.itp, ends with the POSRES_LIGAND section, and then the topology reads the water topology, etc. *This is the structure of my main topology file: ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include topol_A.itp #include topol_B.itp #include topol_C.itp #include topol_D.itp ; Include lipid topology #include popc_Stockner.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound
Re: [gmx-users] Position-restraint
On Jul 28, 2009, at 9:50 AM, Morteza Khabiri wrote: Dear gmx-users, I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the following message: Program grompp, VERSION 3.3 Source code file: toppush.c, line: 1108 Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) The erro is here and has been pointed out to you already. your posre file contains more position restraints than atoms! I sent an email about this yesterday, but the advice was not applicable because of the set-up of my topology file. previous advice: ** Position restraints sections must be placed within the same [ moleculetype ] definition. So, you can't include all of the position restraint information in one file, since that file is part of the Protein [ moleculetype ] definition. The ligand should be placed in its own posre.itp file and included in the topology. These lines must be placed *outside* of the [ moleculetype ] directive of any other molecule(s) in the system. For consistency, whenever I have ligands, I place them immediately after the protein [ moleculetype ] and water topology, i.e.: #ifdef POSRES #include posre.itp #endif #include ligand.itp #ifdef POSRES_LIGAND #include ligand_posre.itp #endif #include spc.itp (etc). That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the ligand section begins with #include ligand.itp, ends with the POSRES_LIGAND section, and then the topology reads the water topology, etc. * This is the structure of my main topology file: ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include topol_A.itp #include topol_B.itp #include topol_C.itp #include topol_D.itp ; Include lipid topology #include popc_Stockner.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 Protein_C 1 Protein_D 1 POPC 288 SOL 33722 NA+ 28 *** At the end of the lipid topology file popc_Stockner.itp, I have placed the #include for the lipid position restraint file posre_lipid.itp. I tried moving the #include for the lipid position restraint into the main topology file, directly after the include lipid topology line, but this gives me the same error. Do you have any suggestions of where exactly to put the #include for the lipid position restraint? Thank you very much untitled-2.html___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] reg mopac.gromacs installations
dear gmx user thanks in advance i have sucessfully installed the folowing version of fft files from src fftw-3.2.2 but when i install the gromacs-4.0.5 by giving the following command LIBS=-lmopac LDFLAGS=-L/usr/lical/lib ./configure --with-qmmm-mopac i got the error as follows configure: error: Cannot find fftw3 library if any one of you know let me know is there is any problem in the path settings? please help me to install successfully i am waiting for your reply soon See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.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] RE:appropriate values fot tau_t and tau_p
Hi, thank you for your help, Berk. The propertie I am looking for is the partial molar volume which can be calculated with this equation and a test particle insertion: vi=V^2exp(-bU)/Vexp(-bU) - V To find out the right mdp parameters I made test runs with a pure box of argon as vapour, so I could calculate the partial molar volume with vi=V/N and compare the results. I tested values for tau_t and tau_p from 0.2 to 10. Then I realized that that I picked a much to small value for the isothermal compressibility and perfomed new runs with values for tau_t and tau_p from 10 to 20. I've chosen ffG43a1 as Force Field. The mdp file I used for the simulations looks like this: ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator =md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1000 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 0.01 emstep = 1 ; Max number of iterations in relax_shells niter= 50 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 1000 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 250 nstenergy= 50 ; Output frequency and precision for xtc file nstxtcout= 1000 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 2.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 2.5 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 2.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 20 ref_t= 115.77 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 20
Re: [gmx-users] Huge acceleration needed to reproduce results!
Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do get is the message ?There were 228 inconsistent shifts. Check your topology? when I carry out the g_msd with the ?mol option but not when I don?t use -mol. Why is this? I also came across a forum post (http://www.mail-archive.com/gmx-users@gromacs.org/msg5.html) that said ?If the distance between two atoms is close to half the box, the force may arbitrarily change sign. This is an ill-defined situation for which there is no obvious solution.? Could this somehow be affecting my simulations? Below are the relevant parts of my .mdp file and other files. If you see something suspicious please let me know because I?m stuck, Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 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= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; 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= epsilon_rf = ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = ; 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= ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 150 ; Pressure coupling Pcoupl = No Pcoupltype = ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= compressibility = ref-p= ; Scaling of reference coordinates, No, All or COM refcoord_scaling = no ; Random seed for Andersen thermostat andersen_seed= ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 150 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR= no ; Relative tolerance of shake shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it
Re: [gmx-users] reg mopac.gromacs installations
vidhya sankar wrote: dear gmx user thanks in advance i have sucessfully installed the folowing version of fft files from src fftw-3.2.2 but when i install the gromacs-4.0.5 by giving the following command LIBS=-lmopac LDFLAGS=-L/usr/lical/lib ./configure --with-qmmm-mopac This command is not only improperly ordered, but it contains a typo in the LDFLAGS. -Justin i got the error as follows *configure: error: Cannot find fftw3 library * if any one of you know let me know is there is any problem in the path settings? please help me to install successfully i am waiting for your reply soon Love Cricket? Check out live scores, photos, video highlights and more. Click here http://in.rd.yahoo.com/tagline_cricket_2/*http://cricket.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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] question about continuation using tpbconv and mdrun -cpi
Hi all, Recently I made some tests on the continuation of gmx 4.0.5. Firstly, I run a complete simulation as the reference. In the full.mdp file, gen_seed=123456 continuation=yes are used to build the same initial structure. In all the simulations, mdrun -dlb no is used because I want to reproduce exactly the same potential energy. 1. Using tpbconv. (part1.mdp is the same as full.mdp except the nsteps) 1a) grompp -s part1 mpirun -np 32 mdrun -deffnm part1 -dlb no tpbconv -s part1.tpr -f part1.trr -e part1.edr -extend 100 -o part2 mpirun -np 32 mdrun -deffnm part2 -dlb no eneconv -f part1.edr part2.edr -o part_all.edr 1b) tpbconv -s part1.tpr -extend 100 -o part2.tpr mpirun -np 32 mdrun -deffnm part2 -cpi part1.cpt -dlb no eneconv -f part1.edr part2.edr -o part_all.edr The potential energy is generated from g_energy, and compared. In this method, I met two problems: Q.a) The potential energies of part2 in both 1a and 1b are not exactly the same as the reference potential! And also the potential of part2 in 1a is different from that in 1b. (Both potentials of part1 from 1a and 1b are identical to the reference.) Q.b) The RMSD of the potential energies of part_all.edr is very big (1 order of magnitude bigger than the corresponding one from the separate .edr files) 2) using mdrun -cpi -append grompp -s full2 mpirun -np 32 mdrun -deffnm full2 -dlb no (stop the job at some time point, then run the following) mpirun -np 32 mdrun -deffnm full2 -dlb no -cpi full2_prev.cpt -append The second (-append) section of the potential energy is also different from the result of the reference potential, even though I am using the same full.mdp file. (the potential in the former section is identical to the reference) Then, how to reproduce exactly the potential? It is said that the continuation from mdrun -cpi is binary identical. However, it seems not in my tests. What's the problem of the very big RMSD of the potential from eneconv? Thanks in advance! regards, Baofu Qiao ___ 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: openmm
Dear all, Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac and Windows so far, and it comes with examples, pretty neat. Even though there's some apparently fixes compared to the usual release of openmm and gromacs-openmm, my molecule didn't work with it yet. Nevertheless, for those with nvidia cuda and Mac or Windows, it's worth trying. Cheers, Alan On Sat, Jul 18, 2009 at 18:31, Alan alanwil...@gmail.com wrote: Thanks Justin. I could swear I tried what you said... anyway it worked now (2.5 x faster), but not with implicit solvent for mdrun-openmm... Trying with plain mdrun with the setup for implicit solvent and it seemed to work (although I don't know how to interpret this from GromacsOpenMMPreview3-Mac/Gromacs-OpenMM Readme.txt file: even though this is not available in the standard Gromacs 4) I still would like an example/tutorial that really worked for someone with gmx openmm. In the end, with mdrun-openmm and implicit solvent in the mdp file, I got a file md.gro full of nan nan. For those interested, here are the commands I did. If you have GMX with ffamber, CUDA and GMX-openmm you may reproduce it. ### cat EOF | em.mdp define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol= 1000.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = Reaction-Field ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step epsilon_rf = 0 pbc = no EOF cat EOF | md.mdp integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.2 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no comm_mode = ANGULAR ; uncomment below to test with implicit solvent ;implicit_solvent = GBSA ;gb_algorithm = OBC ;gb_epsilon_solvent = 78.3 EOF wget -c http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdbcompression=NOstructureId=1BVG -O 1BVG.pdb grep 'ATOM ' 1BVG.pdb| Protein.pdb grep 'HETATM' 1BVG.pdb| Ligand.pdb sed s/PRO\ A\ \ \ 1/NPROA\ \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \ | sed s/PHE\ A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \ | sed s/O\ \ \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \ | sed s/HIS\ /HID\ /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g | ProteinAmber.pdb # Process with pdb2gmx and define water pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -ignh grompp -f em.mdp -c Protein2.pdb -p Protein.top -o em.tpr mdrun -v -deffnm em grompp -f md.mdp -c em.gro -p Protein.top -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr # OK mdrun-openmm -v -deffnm md # 3 times fater # works fine without set for implicit solvent in md.mdp # with implicit solvent, md.gro full of nan nan nan everywhere. ### On Sat, Jul 18, 2009 at 17:31, Alanalanwil...@gmail.com wrote: Ok, I tried. Can someone tell how to have in a mdp file this combination (in order to satisfy gromacs openmm) without raising a error in grompp? ns_type = simple pbc = no coulombtype = Reaction-Field Whatever I try I get: ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented My full md.mdp file is: integrator = md nsteps = 1000 dt = 0.002 constraints = all-bonds nstcomm = 1 ns_type = simple rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 vdwtype = cut-off coulombtype = Reaction-Field epsilon_rf = 0 Tcoupl = no Pcoupl = no gen_vel = yes nstxout = 2 ; write coords every # step lincs-iter = 2 pbc = no implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 comm_mode = ANGULAR Many thanks in advance, Alan On Sat, Jul 18, 2009 at 11:35, Alanalanwil...@gmail.com wrote: Dear
[gmx-users] linking
Dear gromacs users Can anyone of you please tell me as to how I can link ligands or chemical compounds onto proteins at specific locations or active sites and not just randomly placing it? Thank you. Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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
Re: [gmx-users] Huge acceleration needed to reproduce results!
Title indicates you think that you have CH4 in MCM: [ system ] ; Name CH4 in MCM Actual system is MCM in CH4: [ molecules ] ; Compound#mols MCM1 CH4340 .mdp accelerates the CH4: acc-grps = CH4 Now I'm not sure if this is the source of any problem, equal and opposite being true, but you are certainly trying to accelerate the more massive group and it seems like a strange thing to do. Could this be it? Chris. -- original message -- Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do get is the message ?There were 228 inconsistent shifts. Check your topology? when I carry out the g_msd with the ?mol option but not when I don?t use -mol. Why is this? I also came across a forum post (http://www.mail-archive.com/gmx-users@gromacs.org/msg5.html) that said ?If the distance between two atoms is close to half the box, the force may arbitrarily change sign. This is an ill-defined situation for which there is no obvious solution.? Could this somehow be affecting my simulations? Below are the relevant parts of my .mdp file and other files. If you see something suspicious please let me know because I?m stuck, Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 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= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; 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= epsilon_rf = ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = ; 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= ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 150 ; Pressure coupling Pcoupl = No Pcoupltype = ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= compressibility = ref-p= ; Scaling of reference coordinates, No, All or COM refcoord_scaling = no ; Random seed for Andersen thermostat andersen_seed= ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 150 gen_seed = 173529 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm
Re: [gmx-users] linking
P.R.Anand Narayanan wrote: Dear gromacs users Can anyone of you please tell me as to how I can link ligands or chemical compounds onto proteins at specific locations or active sites and not just randomly placing it? ... by doing it. Unfortunately, linking is too vague a verb to get you real help. Please describe what you're trying to achieve more precisely. 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
Re: [gmx-users] Huge acceleration needed to reproduce results!
Hi Chris, Thanks for the input-its good to get another person's perspective. Let me explain a bit more about my system... MCM stands for MCM-41, a mesoporous silica which consits of 1071 atoms so even though it is only 1 molecule, it is the more massive group. I am purposely accelerating the methane to try and calculate their diffusion thourgh the pore of the MCM. As I understand it, the acceleration I specify should be applied to each and every molecule of CH4. I.e if I specify an acceleration of 0.1 nm ps-2, each of my 340 molecules should experience an acceleration of 0.1. I.e the acceleration is not in any way divided up between the total number of accelerated molecules? Jenny Quoting chris.ne...@utoronto.ca: Title indicates you think that you have CH4 in MCM: [ system ] ; Name CH4 in MCM Actual system is MCM in CH4: [ molecules ] ; Compound#mols MCM1 CH4340 .mdp accelerates the CH4: acc-grps = CH4 Now I'm not sure if this is the source of any problem, equal and opposite being true, but you are certainly trying to accelerate the more massive group and it seems like a strange thing to do. Could this be it? Chris. -- original message -- Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do get is the message ?There were 228 inconsistent shifts. Check your topology? when I carry out the g_msd with the ?mol option but not when I don?t use -mol. Why is this? I also came across a forum post (http://www.mail-archive.com/gmx-users@gromacs.org/msg5.html) that said ?If the distance between two atoms is close to half the box, the force may arbitrarily change sign. This is an ill-defined situation for which there is no obvious solution.? Could this somehow be affecting my simulations? Below are the relevant parts of my .mdp file and other files. If you see something suspicious please let me know because I?m stuck, Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 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= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; 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= epsilon_rf = ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = ; 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= ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover ; Groups to couple
Re: [gmx-users] Huge acceleration needed to reproduce results!
As for your posted problem, I don't think that I can be of any more assistance. I picked the low-hanging fruit, but probably you need some assistance from somebody who has actually done constant acceleration simulations. I will take this opportunity to note, though, that you will never get diffusion information from a constant acceleration simulation (as far as I can figure). Although I am certain that you require a resolution to your posted problem, I suggest that you concurrently ensure that your approach is even warranted. Chris. Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hi Chris, Thanks for the input-its good to get another person's perspective. Let me explain a bit more about my system... MCM stands for MCM-41, a mesoporous silica which consits of 1071 atoms so even though it is only 1 molecule, it is the more massive group. I am purposely accelerating the methane to try and calculate their diffusion thourgh the pore of the MCM. As I understand it, the acceleration I specify should be applied to each and every molecule of CH4. I.e if I specify an acceleration of 0.1 nm ps-2, each of my 340 molecules should experience an acceleration of 0.1. I.e the acceleration is not in any way divided up between the total number of accelerated molecules? Jenny Quoting chris.ne...@utoronto.ca: Title indicates you think that you have CH4 in MCM: [ system ] ; Name CH4 in MCM Actual system is MCM in CH4: [ molecules ] ; Compound#mols MCM1 CH4340 .mdp accelerates the CH4: acc-grps = CH4 Now I'm not sure if this is the source of any problem, equal and opposite being true, but you are certainly trying to accelerate the more massive group and it seems like a strange thing to do. Could this be it? Chris. -- original message -- Quoting Jennifer Williams jennifer.willi...@ed.ac.uk: Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do get is the message ?There were 228 inconsistent shifts. Check your topology? when I carry out the g_msd with the ?mol option but not when I don?t use -mol. Why is this? I also came across a forum post (http://www.mail-archive.com/gmx-users@gromacs.org/msg5.html) that said ?If the distance between two atoms is close to half the box, the force may arbitrarily change sign. This is an ill-defined situation for which there is no obvious solution.? Could this somehow be affecting my simulations? Below are the relevant parts of my .mdp file and other files. If you see something suspicious please let me know because I?m stuck, Thanks ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 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= ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file nstxtcout= 1000 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 = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = yes ; 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= epsilon_rf = ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = ;
[gmx-users] energy of individual protein residues
Hello: I am interested in plotting the (kinetic) energy of the individual residues of a protein that I am working with. Is there a straight forward way to do this? Any suggestions would be greatly appreciated! Thank you, Kristina ___ 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] MD Simulation of DPPC Lipid Bilayer
Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation of hydrated dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature (~298 K). Are there tutorials that provide step-by-step instructions on how to do this? Thank you. Nancy ___ 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] MD Simulation of DPPC Lipid Bilayer
Quoting Nancy nancy5vi...@gmail.com: Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation of hydrated dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature (~298 K). Are there tutorials that provide step-by-step instructions on how to do this? Not directly, but there are several resources available. Step 1 should certainly be Chapter 5 of the manual, to understand how to construct the topology of your system, since pdb2gmx will not do it for you. Other than that, there are general references online: http://oldwiki.gromacs.org/index.php/Membrane_Simulations There is also a plethora of question/answer threads in the list archive, which can be searched through the online interface: http://oldwww.gromacs.org/swish-e/search/search2.php Structures and topologies can be downloaded from a number of research group webpages, many of which are cited in the literature and mentioned in the archived discussions. -Justin Thank you. Nancy Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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] MD Simulation of DPPC Lipid Bilayer
I tried to follow the Membrane Protein tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I downloaded the properly oriented PDB file of the KALP-15 model peptide: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/KALP-15_princ.pdb I then attempted to run the pdb2gmx command: pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc For the force field, I chose #4, the GROMOS96 53a6 force field, as well as None for the termini, as stated in the tutorial. However, pdb2gmx outputs the following error message: --- Program pdb2gmx, VERSION 4.0.5 Source code file: pgutil.c, line: 87 Fatal error: Atom H not found in residue 17 while adding improper --- Please let me know how I should go about this. Thanks, Nancy On Tue, Jul 28, 2009 at 1:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Nancy nancy5vi...@gmail.com: Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation of hydrated dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature (~298 K). Are there tutorials that provide step-by-step instructions on how to do this? Not directly, but there are several resources available. Step 1 should certainly be Chapter 5 of the manual, to understand how to construct the topology of your system, since pdb2gmx will not do it for you. Other than that, there are general references online: http://oldwiki.gromacs.org/index.php/Membrane_Simulations There is also a plethora of question/answer threads in the list archive, which can be searched through the online interface: http://oldwww.gromacs.org/swish-e/search/search2.php Structures and topologies can be downloaded from a number of research group webpages, many of which are cited in the literature and mentioned in the archived discussions. -Justin Thank you. Nancy Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@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 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] MD Simulation of DPPC Lipid Bilayer
This is a bug that has been reported some time ago (by me). To fix the issue, in the .rtp entry for [ NH2 ], change the improper line: N H H -C gi_1 to N H1 H2 -C gi_1 -Justin Nancy wrote: I tried to follow the Membrane Protein tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I downloaded the properly oriented PDB file of the KALP-15 model peptide: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/KALP-15_princ.pdb I then attempted to run the pdb2gmx command: pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc For the force field, I chose #4, the GROMOS96 53a6 force field, as well as None for the termini, as stated in the tutorial. However, pdb2gmx outputs the following error message: --- Program pdb2gmx, VERSION 4.0.5 Source code file: pgutil.c, line: 87 Fatal error: Atom H not found in residue 17 while adding improper --- Please let me know how I should go about this. Thanks, Nancy On Tue, Jul 28, 2009 at 1:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Quoting Nancy nancy5vi...@gmail.com mailto:nancy5vi...@gmail.com: Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation of hydrated dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature (~298 K). Are there tutorials that provide step-by-step instructions on how to do this? Not directly, but there are several resources available. Step 1 should certainly be Chapter 5 of the manual, to understand how to construct the topology of your system, since pdb2gmx will not do it for you. Other than that, there are general references online: http://oldwiki.gromacs.org/index.php/Membrane_Simulations There is also a plethora of question/answer threads in the list archive, which can be searched through the online interface: http://oldwww.gromacs.org/swish-e/search/search2.php Structures and topologies can be downloaded from a number of research group webpages, many of which are cited in the literature and mentioned in the archived discussions. -Justin Thank you. Nancy Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalem...@vt.edu mailto:jalem...@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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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] building C-Ter residues : automated
Hi all, I have a bunch of 200 pdb structures with missing C terminal residues , namely OC1 and OC2 due to which I am unable to build a topology file . I would appreciate if anyone knows of a tool or program which is capable of automatically adding these residues in a batch mode rather than manually adding these residues using pymol or swisspdviewer etc. Thanks, Lorraine. ___ 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] building C-Ter residues : automated
lorna mendonca wrote: Hi all, I have a bunch of 200 pdb structures with missing C terminal residues , namely OC1 and OC2 due to which I am unable to build a topology file . I would appreciate if anyone knows of a tool or program which is capable of automatically adding these residues in a batch mode rather than manually adding these residues using pymol or swisspdviewer etc. A correctly formatted C-terminal database for the right forcefield should be capable of building those two atoms - see section 5.6.3 of the manual. Then you can script pdb2gmx to build these atoms and incidentally produce topologies. The advice here http://oldwiki.gromacs.org/index.php/Making_Commands_Non-Interactive may help. 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
Re: [gmx-users] energy of individual protein residues
Kristina Woods wrote: Hello: I am interested in plotting the (kinetic) energy of the individual residues of a protein that I am working with. Is there a straight forward way to do this? Any suggestions would be greatly appreciated! g_traj -h. You may need to supply an index file with groups for each residue. 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
Re: [gmx-users] question about continuation using tpbconv and mdrun -cpi
Baofu Qiao wrote: Hi all, Recently I made some tests on the continuation of gmx 4.0.5. Firstly, I run a complete simulation as the reference. In the full.mdp file, gen_seed=123456 continuation=yes are used to build the same initial structure. In all the simulations, mdrun -dlb no is used because I want to reproduce exactly the same potential energy. 1. Using tpbconv. (part1.mdp is the same as full.mdp except the nsteps) 1a) grompp -s part1 mpirun -np 32 mdrun -deffnm part1 -dlb no tpbconv -s part1.tpr -f part1.trr -e part1.edr -extend 100 -o part2 mpirun -np 32 mdrun -deffnm part2 -dlb no eneconv -f part1.edr part2.edr -o part_all.edr 1b) tpbconv -s part1.tpr -extend 100 -o part2.tpr mpirun -np 32 mdrun -deffnm part2 -cpi part1.cpt -dlb no eneconv -f part1.edr part2.edr -o part_all.edr The potential energy is generated from g_energy, and compared. In this method, I met two problems: Q.a) The potential energies of part2 in both 1a and 1b are not exactly the same as the reference potential! And also the potential of part2 in 1a is different from that in 1b. (Both potentials of part1 from 1a and 1b are identical to the reference.) Q.b) The RMSD of the potential energies of part_all.edr is very big (1 order of magnitude bigger than the corresponding one from the separate .edr files) 2) using mdrun -cpi -append grompp -s full2 mpirun -np 32 mdrun -deffnm full2 -dlb no (stop the job at some time point, then run the following) mpirun -np 32 mdrun -deffnm full2 -dlb no -cpi full2_prev.cpt -append The second (-append) section of the potential energy is also different from the result of the reference potential, even though I am using the same full.mdp file. (the potential in the former section is identical to the reference) Then, how to reproduce exactly the potential? While mdrun -dlb no is a good start, mdrun -reprod takes care of some other things too... It is said that the continuation from mdrun -cpi is binary identical. Not quite... it's an exact restart from the old point in the ensemble, but the manner in which mdrun does future integration is only reproducible if you force it to be so. However, it seems not in my tests. What's the problem of the very big RMSD of the potential from eneconv? Not sure. 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
