Re: [gmx-users] A question about deuteriu order parameters graph
Hi Alex You're running just 1ns, which is actually too short for production in this kind of systems. Enlarge the simulation time (e.g. up to 50ns) and see if you get a more reasonable Scd plots. Javier El 08/11/11 21:40, Alex Jemulin escribió: Dear Javier Here is mdp file for MD run title= cxcr7-DPPC Production MD ; Run parameters integrator= md; leap-frog integrator nsteps= 50; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 p nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2; short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= Nose-Hoover; More accurate thermostat tc-grps= Protein DPPCSOL_NA; three coupling groups - more accurate tau_t= 0.50.50.5; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 2.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_NA Here are some graphs I made after MD run: g_energy -f md_0_1.edr -o temperature_MD.xvg http://www.freeimagehosting.net/ca04e g_energy -f md_0_1.edr -o pressione_MD.xvg http://www.freeimagehosting.net/d3387 g_energy -f md_0_1.edr -o totenergia_MD.xvg http://www.freeimagehosting.net/108a7 Here are commands for calculating deuterium order parameters make_ndx -f md_0_1.tpr -o sn1.ndx a C34 a C36 a C37 a C38 ... a C50 del 0-21 q g_order -s md_0_1.tpr -f md_0_1.xtc -n sn1.ndx -d z -od deuter_sn1.xvg make_ndx -f md_0_1.tpr -o sn2.ndx carbons C17-C31 del 0-21 q g_order -s md_0_1.tpr -f md_0_1.xtc -n sn2.ndx -d z -od deuter_sn2.xvg Thank your very much for your support Bests *Da:* Javier Cerezo j...@um.es *A:* gmx-users@gromacs.org *Inviato:* Martedì 8 Novembre 2011 9:45 *Oggetto:* Re: [gmx-users] A question about deuteriu order parameters graph Hi Alex Deuterium order parameter is a property related to the relative orientation of molecular axis taking the bilayer normal as reference. How to use them to extract useful structural information is a matter of how you interpret the values regarding their definition (see e.g. Egberts and Berendsen [J. Chem. Phys.(1988), vol 89, 3718] or Heller et al [J. Phys. Chem. (1993), vol 97, 8343]). In general, by comparing order parameters of different systems you can have some hints about the phase or ordering of your different systems and how it may change (for example at different temperature or after insertion of a membrane protein). Morover, the usefulness of this paramenter mainly comes from the fact that they are readily available from simulations and thus can be used to validate your methodology. Concretely, experimental information about the deuterium order parameter (Scd, the one you reported) is spread over the scientific literature about membranes (see e.g. the series of papers from the J.F Nagle's group) and it is the deuterium order parameter commonly reported in MD simulations. For the case of DPPC you can take for
[gmx-users] diffusion through nanotube
Hello, I am studying the diffusion of a small molecule through a cyclic peptide based nanotube using pull code, here is my code for pulling, pull= umbrella pull_geometry = position pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = Protein pull_group1 = FLU pull_rate1 = 0.005 pull_k1 = 1000 my reference group is a nanotube and pulling group is a small molecule. In this study, should I have to apply position restraint for the protein molecules? Regards, Vijay. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_mindist -on
Dear gmx Users, I am wondering what is the value of Number of Contacts (0.6 nm) between two groups. When I specify one group - Ligand and second - protein residue - does it count every dostance within 0.6 nm between every atom from one group and every atom from the second specified group? Cheers, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] about the velocity output from leap-frog integrators
Hello users, I have few conflicting answers from the user mailing list about the following question. Using leap-frog integrator, what is the velocity that is WRITTEN in the trajectory file for a frame corresponding to r(t)? Is it v(t-dt/2) or v(t). Has the protocol for writing velocity in trajectory file been consistent from version 3.x to 4.5.x? Here are few posts hinting its v(t): http://lists.gromacs.org/pipermail/gmx-users/2002-July/001969.html http://lists.gromacs.org/pipermail/gmx-users/2003-September/006956.html Here are couple of posts hinting its v(t-dt/2): http://lists.gromacs.org/pipermail/gmx-users/2006-June/022261.html http://lists.gromacs.org/pipermail/gmx-users/2003-March/004827.html Please let me know. The problem is with certain class of simulations of bounded flows, these two definitions provide contrasting results for suitably averaged velocity. Sincerely Ravi Bhadauria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
回复： [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao)
Dear sir: this is my BASENAME.ORCAINFO: ! rks b3lyp svp tightscf opt grid4 nofinalgrid ! normalprint ! rijcosx sv/j *xyz -1 2 S 2.983 3.527 3.279 C 3.007 3.497 3.463 C 3.156 3.478 3.230 C 3.174 3.484 3.088 O 3.236 3.446 3.317 C 3.296 3.455 3.037 C 3.338 3.447 2.901 C 3.473 3.421 2.865 C 3.520 3.429 2.736 C 3.426 3.460 2.629 C 3.291 3.474 2.666 C 3.248 3.466 2.795 H 3.102 3.541 3.489 H 2.938 3.561 3.515 LA 3.005 3.402 3.492 H 3.094 3.510 3.023 H 3.375 3.437 3.113 H 3.543 3.399 2.942 H 3.623 3.409 2.711 O 3.460 3.469 2.507 H 3.223 3.491 2.585 H 3.143 3.475 2.810 * in fact, the stand-alone version of Orca can normal calculates it, of course, LA must be replaced by DA ( dummy atom in ORCA), but if use LA in gromacs/ORCA, Unless this is specifically allowed this means that the basis set is not available for this element - Aborting the run --- 11年11月9日，周三, Gerrit Groenhof ggro...@gwdg.de 写道： 发件人: Gerrit Groenhof ggro...@gwdg.de 主题: [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月9日,周三,下午3:30 Did you run also your QM subsystem with the stand-alone version of Orca? 6. ORCA and dummy atom in the gromacs (xi zhao) Gerrit -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to list OPLS parameters
Hi all, for a publication i want to list the used OPLS parameters for the investigated molecules. In GROMACS all atomtypes are uniquely defined by the atomtype `opls_xyz`. And from the atomtypes one can deduct the bonded parameters. So it is sufficient to list only the atomtypes and probably charges. My question is now, is this definition common knowledge, or only GROMACS-intern? From the header of `ffoplsaa.atp` one sees that the first 65 atomtypes are for the OPLS-UA force field, and the names of the atomtypes are the same as in the paper which is mentioned. Concerning the OPLS-AA force field, is there the GROMACS numbering scheme also common knowledge? Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PLUMED release 1.3 available
The PLUMED Developers Team is proud to announce that the NEW version of PLUMED 1.3 is available at www.plumed-code.org 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 and ab-initio molecular dynamics codes. PLUMED provides easy access to umbrella sampling, metadynamics, steered md and many other enhanced sampling and free-energy methods. In this new release: * New Features: - Reconaissance Metadynamics - Driven adiabatic free energy dynamics - Python interface - Function of CVs - Tool for unbiasing well-tempered metadynamics calculations - Projection of gradient of CVs - Tool to perform bias-exchange simulations via linux shell with every MD engine - New INTERVAL keyword to limit the sampling along a CV * New Collective Variables: - PCA - SPRINT topological variables - Radial and angular distribution function - Gyration tensor based CVs * New Supported Codes: - Cpmd 3.15.1 - Namd 2.8 - Amber 11 - Gromacs 4.5.5 - Quantum-ESPRESSO 4.3.2 - Lammps 27-10-2011 - ACEMD 1.2 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MD structure analysis
Greeting After finishing a M.D simulation an ensuring that equilibration of the protein is done in its solvent cube according to RMS, potential energy ,temperature , pressure , radius of gyration ... etc what structure should i use for analysis ? is it the average structure of some few last nanoseconds of the simulation , OR the structure of the last frame in simulation, and is there any special cases where one of the two cited structures could insight more than the other ? ( for example : for Hydrogen bonds is the average structure more suitable for analysis than the last frame ? ...) Thanks :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MD structure analysis
larif sofiene wrote: Greeting After finishing a M.D simulation an ensuring that equilibration of the protein is done in its solvent cube according to RMS, potential energy ,temperature , pressure , radius of gyration ... etc what structure should i use for analysis ? is it the average structure of some few last nanoseconds of the simulation , OR the structure of the last frame in simulation, and is there any special cases where one of the two cited structures could insight more than the other ? ( for example : for Hydrogen bonds is the average structure more suitable for analysis than the last frame ? ...) A single structure should not be used for analysis, and you will likely find that an average structure has very little meaning. http://www.gromacs.org/Documentation/Terminology/Average_Structure You should measure the observables of interest based on the question posed prior to running the simulation, then average these relevant data over the equilibrated time period. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error with pdb input
Hello I got the following error (my command is pdb2gmx -f coord.pdb -water tip3p ) : Warning: Number of atoms in coord.pdb is 0 Software inconsistency error: Trying to deduce atomnumbers when no pdb information is present My pdb file has the following structure HEADER my molecules name ATOM 1 5.33618975678115 -0.07916062770658 1.39429663262701 n ATOM 2 6.73371782109540 -2.15676333272371 0.62908982963763 c ATOM 3 9.03483733311025 -2.20332618463802 0.65509246122614 o ATOM 4 5.38645647191591 -4.30702600755030 -0.22693721129824 n ATOM 5 2.79934580695015 -4.52186897159807 -0.44786509349390 c ATOM 6 1.68306568299327 -6.40460311779204 -1.24068079528474 o ATOM 7 1.48545702127742 -2.26124629061096 0.37342878111953 c The numbers are cartesian coordinates in Bohrs Thanks for help Regards Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] barostat for gases
Looks generally reasonable. Thanks! - Vitaly On Tue, Nov 8, 2011 at 12:20 PM, Krzysztof Kuczera kkucz...@ku.edu wrote: The ideal gas result is -(1/V)(dV/dp)_T = 1/p , so I suppose the value should be = 1.0 bar-1 under standard conditions Krzysztof On 11/8/11 10:51 AM, Dr. Vitaly V. Chaban wrote: Could anybody please suggest a convenient compressibility value for MD boxes of gases (at normal conditions)? Thanks. -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with pdb input
Lara Bunte wrote: Hello I got the following error (my command is pdb2gmx -f coord.pdb -water tip3p ) : Warning: Number of atoms in coord.pdb is 0 Software inconsistency error: Trying to deduce atomnumbers when no pdb information is present My pdb file has the following structure HEADER my molecules name ATOM 15.33618975678115 -0.07916062770658 1.39429663262701 n ATOM 26.73371782109540 -2.15676333272371 0.62908982963763 c ATOM 39.03483733311025 -2.20332618463802 0.65509246122614 o ATOM 45.38645647191591 -4.30702600755030 -0.22693721129824 n ATOM 52.79934580695015 -4.52186897159807 -0.44786509349390 c ATOM 61.68306568299327 -6.40460311779204 -1.24068079528474 o ATOM 71.48545702127742 -2.26124629061096 0.37342878111953 c The numbers are cartesian coordinates in Bohrs The file does not follow standard PDB format, which is required by all Gromacs programs to function properly. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where is Coul-LR?
So would it be reasonable to set rcoulomb = 2 or even 3 nm when rerunning a trajectory? I am looking at a ligand-antibody system, and I guess the long-range electrostatic interactions will not be small. A trick proposed by Nicolas in the mailing list during 2007 is to set charges to 0.00 for everything except the atoms we are interested in. This would make Coul-LR: = Coul.-recip., which is calculated by PME (more accurate than just setting rcoulomb to 3nm?) and we can read from .edr file. So I wonder if this method is theoretically sound? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
I've another question about NMA. 1- As I understood the Sparce matrix method is used on default in case when my reference structure consist of alot of atoms. If this true the output Hessian.mtx would be in sparce format, wouldn't it ? 2- How I can convert output.mtx to the txt format ? As the consequence I want to obtain something like this http://www.csb.pitt.edu/prody/_downloads/oanm_hes.txt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Parametrisation of the heteroatomic pdb
Justin, Could you tell me another alternative ways to replace existing cap groups in my pdb besides xleap ? ( I've had many problems with the pdb's processed by this soft). Also I've tried to make topology for the non-standart caps by PRODRG but I also have some problems with such parametrisation. Also I've not found suitable topology for some D-isomers ( it's strange that parametriation for such typical non-standart residues is absent in all force fields ). As I understood I cant use topology of L-analogs for the parametrisation of such D-forms because I dont know suitable parameters for dihedrals for instance. Have someone pre-built parameters for the D-aa for Gromos or Charmm force field? Thanks, James 2011/10/29 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, hello! Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ? xleap At this point, please start a new thread for your questions, as these topics are completely unrelated to where you started. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Parametrisation of the heteroatomic pdb
James Starlight wrote: Justin, Could you tell me another alternative ways to replace existing cap groups in my pdb besides xleap ? ( I've had many problems with the pdb's processed by this soft). Also I've tried to make topology for the non-standart caps by PRODRG but I also have some problems with such parametrisation. Unless you describe your problems, there's very little anyone can or will try to do to help you. I've never had a problem with an xleap coordinate file, so I can't offer you any additional guidance with that. Otherwise, there are dozens of programs that are capable of drawing molecules or editing files. See, for instance: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources -Justin Also I've not found suitable topology for some D-isomers ( it's strange that parametriation for such typical non-standart residues is absent in all force fields ). As I understood I cant use topology of L-analogs for the parametrisation of such D-forms because I dont know suitable parameters for dihedrals for instance. Have someone pre-built parameters for the D-aa for Gromos or Charmm force field? Thanks, James 2011/10/29 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, hello! Could you tell me what exactly program from the Amber tools package you've used for the KALP peptide preparation e.g for capping ? xleap At this point, please start a new thread for your questions, as these topics are completely unrelated to where you started. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with pdb input
Please keep the discussion on the list. Lara Bunte wrote: Hi what is wrong in the format or what do I have to change. Please don't give me a link to the pdb site, I do not understand it :-( The PDB format requires certain columns with the prescribed information be present at the specified spacing. Since you won't allow me to point you to the site that has the walkthrough on how to interpret the contents, then the best I will offer you is to download any protein structure from the PDB and look at it. You will see dramatic differences between the required format and what you have attempted to use. A small example is available in the online manual, but opening the files in a text editor to clearly see the spacing is preferred. http://manual.gromacs.org/online/pdb.html -Justin regards Lara *Von:* Justin A. Lemkul jalem...@vt.edu *An:* Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org *Gesendet:* 19:02 Mittwoch, 9.November 2011 *Betreff:* Re: [gmx-users] Error with pdb input Lara Bunte wrote: Hello I got the following error (my command is pdb2gmx -f coord.pdb -water tip3p ) : Warning: Number of atoms in coord.pdb is 0 Software inconsistency error: Trying to deduce atomnumbers when no pdb information is present My pdb file has the following structure HEADER my molecules name ATOM 15.33618975678115-0.07916062770658 1.39429663262701 n ATOM 26.73371782109540-2.15676333272371 0.62908982963763 c ATOM 39.03483733311025-2.20332618463802 0.65509246122614 o ATOM 45.38645647191591-4.30702600755030-0.22693721129824 n ATOM 52.79934580695015-4.52186897159807-0.44786509349390 c ATOM 61.68306568299327-6.40460311779204-1.24068079528474 o ATOM 71.48545702127742-2.26124629061096 0.37342878111953 c The numbers are cartesian coordinates in Bohrs The file does not follow standard PDB format, which is required by all Gromacs programs to function properly. -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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Using CHARMM 36 for DPPC simulation
5Hello all, I am trying to use CHARMM 36 for DPPC membrane simulation. I did the following so far: 1. Download pdb file containing 128 DPPC molecules from http://www.charmm-gui.org/?doc=archivelib=lipid_pure 2. I separated one lipid molecule from the obtained pdb file and used pdb2gmx -f 1dppc.gro -nochargegrp The top file obtained was converted to itp file by commenting few things out. 3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer from CHARMM GUI for the box length. I used editconf to convert the pdb to gro and manually inserted the box size in the gro file. 4. Created a system.top file which looks like #include charmm36.ff/forcefield.itp #include lipid.itp #include charmm36.ff/tips3p.itp [ system ] chol [ molecules ] DPPC 128 SOL 3659 5. I used following mdp settings integrator = md ; leap-frog integrator nsteps = 2000 ; 40 ns dt = 0.002 ; 2 fs ; Output control nstxout = 10 ; save coordinates every 200 ps nstvout = 10 ; save velocities every 200 ps nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 vdwtype = switch rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw_switch = 0.8 ; Electrostatics rcoulomb= 1.0 rcoulomb_switch = 0.0 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 6 ; cubic interpolation fourierspacing = 0.15 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = DPPC SOL ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 323.15 323.15 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = No ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes gen_temp= 200.0 gen_seed= 173529 ; COM motion removal nstcomm = 1 comm-mode = Linear comm-grps = DPPC SOL ; Energy monitoring energygrps = DPPC SOL ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy The resulting simulation gave me an area per lipid =0.591 nm^2. This is not quite right. Can somebody suggest what else could i do it get close to the 0.63 nm^2 value. Also when i looked at trajectory file it seemed that the box length was not set up quite right because the downloaded pdb file looked ok with the membrane in the middle but at the next frame the membrane was at a totally different location. The leaflets were separated and the middle of the membrane was at the edge of the box. Also when i used pdb2gmx -nochargegrp on the downloaded file it created a gro file whose system size was 8.20170 8.64120 6.54740 in contrast to6.4 6.4 6.38452 . Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to list OPLS parameters
On 10/11/2011 12:52 AM, Thomas Schlesier wrote: Hi all, for a publication i want to list the used OPLS parameters for the investigated molecules. In GROMACS all atomtypes are uniquely defined by the atomtype `opls_xyz`. And from the atomtypes one can deduct the bonded parameters. So it is sufficient to list only the atomtypes and probably charges. My question is now, is this definition common knowledge, or only GROMACS-intern? From the header of `ffoplsaa.atp` one sees that the first 65 atomtypes are for the OPLS-UA force field, and the names of the atomtypes are the same as in the paper which is mentioned. Concerning the OPLS-AA force field, is there the GROMACS numbering scheme also common knowledge? If you consult the paper in which OPLS-AA was published (which you no doubt read before simulating with OPLS-AA), you will see that the numbering scheme is not internal to GROMACS. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] where is Coul-LR?
On 10/11/2011 6:03 AM, Yun Shi wrote: So would it be reasonable to set rcoulomb = 2 or even 3 nm when rerunning a trajectory? I am looking at a ligand-antibody system, and I guess the long-range electrostatic interactions will not be small. You can set rcoulomb to anything you like, but there's no reason to suppose the value of the computed Coulomb energy has any connection to a relevant observable. The force field was not designed to work at the cutoff values you suggest, and a longer cutoff is not necessarily more accurate. Neither was the force field parametrized to be able to be decomposed this way. A trick proposed by Nicolas in the mailing list during 2007 is to set charges to 0.00 for everything except the atoms we are interested in. This would make Coul-LR: = Coul.-recip., which is calculated by PME (more accurate than just setting rcoulomb to 3nm?) and we can read from .edr file. So I wonder if this method is theoretically sound? There is no sense in which Coul-LR relates to Coul-recip. They are computed in fundamentally different ways, and affect Coul-SR differently too. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
On 10/11/2011 6:48 AM, James Starlight wrote: I've another question about NMA. 1- As I understood the Sparce matrix method is used on default in case when my reference structure consist of alot of atoms. If this true the output Hessian.mtx would be in sparce format, wouldn't it ? 2- How I can convert output.mtx to the txt format ? As the consequence I want to obtain something like this http://www.csb.pitt.edu/prody/_downloads/oanm_hes.txt GROMACS is not very helpful with matrices of data, unfortunately. You can dump the numbers out of the .mtx format with gmxdump, but you would be on your own to then convert it to some other format you want (i.e. write some script). 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re: PBC - Protein - ligand
Sounds like the ligand is near the edge of the box, so only has to move short distance then does the jumping you are observing. The suggestion that has already been make, -pbc nojump, should stop that. Another option is to center the box on a residue within the protein which is near the spot at which the ligand is interacting. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Steven Neumann Sent: Tuesday, 8 November 2011 8:30 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] Re: PBC - Protein - ligand Thank you Justin, Mark and Tsjerk. I used the following workflow trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol trjconv -s md.tpr -f pbc_fix.xtc -n index.ndx -pbc cluster -o pbcfixcluster.xtc (Protein+ligand group) trjconv -s md.tpr -f pbcfixcluster.xtc -o center.xtc -center (center on the protein) trjconv -s md.tpr -f center.xtc -o Cluster1.xtc -fit rot+trans (choose protein for fitting) Trajectory looks very good from the time when ligand stacked to the protein (90% of trajectory) but at the begining of the trajectory (when it is away from protein) it still jumps. I think that is the best solution I have found. If you know how to fix begining please let me know. Steven On Tue, Nov 8, 2011 at 8:53 AM, Steven Neumann s.neuman...@gmail.commailto:s.neuman...@gmail.com wrote: On Mon, Nov 7, 2011 at 9:47 PM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu wrote: Steven Neumann wrote: Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my ligand close to protein but sometimes still changing its position rapidly... No clue for now how to solve it... I have no idea why the proposed protocol isn't working, but I know that one should be able to do something very simple, along the lines of the following, for this to work: 1. trjconv -s md.tpr -f md.xtc -o pbc_fix.xtc -pbc mol 2. trjconv -s md.tpr -f pbc_fix.xtc -o center.xtc -center (center on the protein) 3. trjconv -s md.tpr -f center.xtc -o fit.xtc -fit rot+trans (choose protein for fitting) -Justin Thank you Justin. From this workflow my ligand is binding the protein most of the frames but sometimes it rapidly jumps to different part of the box and come back again. Then remains with protein and situation is repeated: in one frame it changes its position and come back to protein remaining. :( no clue... Steven On Monday, November 7, 2011, Tsjerk Wassenaar tsje...@gmail.commailto:tsje...@gmail.com mailto:tsje...@gmail.commailto:tsje...@gmail.com wrote: Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that the ligand is really with the protein and not in the solvent... Cheers, Tsjerk On Mon, Nov 7, 2011 at 5:17 PM, Steven Neumann s.neuman...@gmail.commailto:s.neuman...@gmail.com mailto:s.neuman...@gmail.commailto:s.neuman...@gmail.com wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu mailto:jalem...@vt.edumailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use |trjconv -|pbc| nojump| after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option
[gmx-users] sudden drop of minimal periodic distance
Hello everyone, I am using g_mindist with -pi option to look at the minimal distance between periodic images of my protein-ligand system. It appears that after a certain amount of time (12 ns or 30 ns or ...), there would be a sudden drop of min distance from well above 2 nm to around 0.15 nm. I wonder if this is caused by the octahedral box I used in the MD simulation. But should I still be able to keep the part of trajectory before the sudden drop as valid so that I could do some analysis with my system? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: sudden drop of minimal periodic distance
Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm, the min periodic image dist still dropped abruptly to 0.172 or something like this after around 35 ns or 30 ns (different trajectory with same topology). So I wonder if this is just inevitable and we should live with it? Thanks, Yun On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi yunsh...@gmail.com wrote: Hello everyone, I am using g_mindist with -pi option to look at the minimal distance between periodic images of my protein-ligand system. It appears that after a certain amount of time (12 ns or 30 ns or ...), there would be a sudden drop of min distance from well above 2 nm to around 0.15 nm. I wonder if this is caused by the octahedral box I used in the MD simulation. But should I still be able to keep the part of trajectory before the sudden drop as valid so that I could do some analysis with my system? Thanks, Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] orca question and LA
Dear Sir: How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp pyp_qm.out' No atoms to convert in Cartesian2Internal ; When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified! Kind regards! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] remd with different potential at different temperature
Hi, this is currently not possible. Currently you can only do temperature or Hamiltonian RepEx. As far as I know 4.6 will support both simultaneous. In the mean time you might be able to accomplish your goal by reformulating the Temp-RepEx as a Hamiltonian RepEx as is done in the newer version of REST. Roland 2011/11/8 杜波 2008d...@gmail.com dear teacher, if i want to do remd with different tabulated potentials. how can i use the mdrun's -table (-table table.xvg -tableb table.xvg )? if it can also use like that,there is another question: and how can i rename the tables name ( table_CR1_CR1: i rename them table_CR1_CR10,table_CR1_CR11,table_CR1_CR12..., i test this is wrong!!! ) thanks regards, PHD, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com mailto:2008d...@gmail.com Message: 1 Date: Tue, 08 Nov 2011 17:55:49 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] remd with different potential at different temperature To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4eb8d275.2010...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 8/11/2011 5:43 PM, ?? wrote: dear teacher, how can i do remd with different non-bond potential at different temperature ? easy to say ,can i use different *.top at diferent temperature. Probably. Try a simple case and see. The REMD implementation checks only certain critical quantities are constant over the generalized ensemble. See the lines that begin Multi-checking in an REMD .log file. You can probably even use different tabulated potentials for each replica. Mark if not ,can you give me some suggestions to rewrite the gromacs codes. thanks!! regards, PHD, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com mailto:2008d...@gmail.com -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to do remd with different tabulated potentials
Hi, for Hamiltonian RepEx you need to formulate the different states as a function of lambda. Look at the free energy documentation to see how to describe different tables for different lambdas. Roland 2011/11/8 杜波 2008d...@gmail.com dear teacher, if i want to do remd with different tabulated potentials. how can i use the mdrun's -table (-table table.xvg -tableb table.xvg )? if it can also use like that,there is another question: and how can i rename the tables name ( table_CR1_CR1: i rename them table_CR1_CR10,table_CR1_CR11,table_CR1_CR12..., i test this is wrong!!! ) thanks regards, PHD, Bo Du Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 E-mail: 2008d...@gmail.com mailto:2008d...@gmail.com -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: sudden drop of minimal periodic distance
Hi Yun, Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before using g_mindist. Also visually check a frame that is reported to have closed contacts. Hope it helps, Tsjerk On Nov 10, 2011 1:45 AM, Yun Shi yunsh...@gmail.com wrote: Sorry, I just found that even if I use a dodecahedron box with -d 1.2 nm, the min periodic image dist still dropped abruptly to 0.172 or something like this after around 35 ns or 30 ns (different trajectory with same topology). So I wonder if this is just inevitable and we should live with it? Thanks, Yun On Wed, Nov 9, 2011 at 4:18 PM, Yun Shi yunsh...@gmail.com wrote: Hello everyone, I am ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_mindist -on
On 9/11/2011 9:09 PM, Steven Neumann wrote: Dear gmx Users, I am wondering what is the value of Number of Contacts (0.6 nm) between two groups. When I specify one group - Ligand and second - protein residue - does it count every dostance within 0.6 nm between every atom from one group and every atom from the second specified group? Does g_mindist -h answer your question? If not, how can the text be improved? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
Thank you, Mark. By the way, also I have some question about data analysing From g_anaeig I can obtain atom fluctuations along defined mode 1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along modes from n to k ) in one graph ? 2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only from full atomic model ? E.g on start g_anaeig ask me Select an index group of 6518 elements that corresponds to the eigenvectors Group 0 ( System) has 6518 elements Group 1 (Protein) has 6518 elements Group 2 ( Protein-H) has 3269 elements Group 3 (C-alpha) has 413 elements Group 4 ( Backbone) has 1239 elements ... but I can chose only full atomic representation of the system consisted of 6518 atoms and any other selection would produce error. Is there any other way to obtain fluctuations on reduced number of atoms from full-atomic system ? 3- Also I've done two different NMA from one reference ( for full atomic model and for C-alpha mode). The overal picture of RMSF for instance was overal in both of the analysis but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues). Why that difference might occur? Is there any way to increase amplitude of fluctuations by the temperature rising for instance ? Thanks, James 2011/11/10 Mark Abraham mark.abra...@anu.edu.au On 10/11/2011 6:48 AM, James Starlight wrote: I've another question about NMA. 1- As I understood the Sparce matrix method is used on default in case when my reference structure consist of alot of atoms. If this true the output Hessian.mtx would be in sparce format, wouldn't it ? 2- How I can convert output.mtx to the txt format ? As the consequence I want to obtain something like this http://www.csb.pitt.edu/prody/**_downloads/oanm_hes.txthttp://www.csb.pitt.edu/prody/_downloads/oanm_hes.txt GROMACS is not very helpful with matrices of data, unfortunately. You can dump the numbers out of the .mtx format with gmxdump, but you would be on your own to then convert it to some other format you want (i.e. write some script). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
On 10/11/2011 5:36 PM, James Starlight wrote: Thank you, Mark. By the way, also I have some question about data analysing From g_anaeig I can obtain atom fluctuations along defined mode 1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along modes from n to k ) in one graph ? Yes, through suitable use of your graphing program on multiple input files. IMO that would not be a suitable discussion for this list. Suggestions for graphing programs and some tricks of the trade are on the GROMACS webpage. 2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only from full atomic model ? E.g on start g_anaeig ask me Select an index group of 6518 elements that corresponds to the eigenvectors Group 0 ( System) has 6518 elements Group 1 (Protein) has 6518 elements Group 2 ( Protein-H) has 3269 elements Group 3 (C-alpha) has 413 elements Group 4 ( Backbone) has 1239 elements ... but I can chose only full atomic representation of the system consisted of 6518 atoms and any other selection would produce error. Is there any other way to obtain fluctuations on reduced number of atoms from full-atomic system ? Unless g_nmeig can be persuaded to calculate on a subset of the Hessian, I would guess not. 3- Also I've done two different NMA from one reference ( for full atomic model and for C-alpha mode). The overal picture of RMSF for instance was overal in both of the analysis but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues). Why that difference might occur? From your description, I think you're comparing apples with oranges. Is there any way to increase amplitude of fluctuations by the temperature rising for instance ? NMA is athermal. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
Mark hello, 2011/11/10 Mark Abraham mark.abra...@anu.edu.au From your description, I think you're comparing apples with oranges. I just want compare results of coarse grained NMA based on C-alpha only with full atomic NMA. I've already done that work and obtain that 1- overal picture of fluctuations is the same for both methods 2- in case of full atomic NMA overal motion is damped in comparison to the C-alpha only NMA ( rmsf of fluctuations are greater in 10 times) 3 Finally I just want to obtain fluctuations on Calpha atoms only for my full atomic NMA for better comparison with cg NMA (e.g representation on one graph RMSF on Calpha atoms only for both methods ) James Is there any way to increase amplitude of fluctuations by the temperature rising for instance ? NMA is athermal. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
Hi James, 1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along modes from n to k ) in one graph ? The total fluctuation is the sum of the fluctuations along all the modes. To get what you want, you just need to some the fluctuations. Alternatively, you can filter a trajectory using a set of modes and do further analysis on that. 2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only from full atomic model ? See the answer above. but I can chose only full atomic representation of the system consisted of 6518 atoms and any other selection would produce error. Is there any other way to obtain fluctuations on reduced number of atoms from full-atomic system ? g_anaeig needs the atoms to match with the eigenvectors, which pertain to the full set of atoms. 3- Also I've done two different NMA from one reference ( for full atomic model and for C-alpha mode). The overal picture of RMSF for instance was overal in both of the analysis but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues). Why that difference might occur? Is there any way to increase amplitude of fluctuations by the temperature rising for instance ? The c-alphas are less hindered in the second model due to the absence of the side chains and such. There's just more freedom. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
Hi Tsjerk, Thanks for help. So as I understood if I want to calculate fluctuations only for Calpha I must first to do NMA of my reference in some mode subspace consisted of the eigenvectors for Calpha atoms only. Does this correct ? Previously I've done something like this for random subspace of modes in MMTK (just to reduce the space for calculation) but how perform such operation in Gromacs I havent known yet :) The c-alphas are less hindered in the second model due to the absence of the side chains and such. There's just more freedom. It's known that solevnt for instance could significant damp motions from normal modes. So in my case It seems that sidechains act as the solvent. How do you think may sidechains not only damp motions oberved for C-alpha atoms merely but also change the trajectory of their motion? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
