[gmx-users] g_analyze doubt
Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. 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] PCA depends of the number of frames?
Hi Ricardo For the case (1) and (2) the most representative structure was used in the option -s ( One that has the lowest rmsd with respect to the average of each cluster). In case (3) the initial structure of the MD was used in the option -s. If all belong to the same system, it is better to use one reference structure, to define the conformational space in the same way, allowing direct comparison. When I look the eigenvalues for the case (1) and (2), I found that the eigenvalue is zero only after index=number of frames (see below) In the case (3) the distribution is smooth I could expect a similar distribution for the case (1) and (2), because the frames are representative of the dymanics of the protein. Why this difference? PCA depend of the number of frames? Yes, it does. This has, in fact, been pointed out in the early papers on PCA in MD. I think it's best to read up more about PCA, including some introductory material from statistics. One thing I'll give away though... ;) Consider the motion of a particle in three dimensions. If you have two frames, you can say something about motion along a line. You need two frames to say something about motion in a plane, and you need at least three points to say something about motion in all three dimensions. Now in your case, each conformation is one point and the conformational space in which the point moves has 3N dimensions. If you have two points, you can only say something about motion along a line, i.e., you have one component with nonzero eigenvector. With three points (conformations), you can obtain two eigenvectors, which span a plane, etc. Hope it helps, 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] PCA depends of the number of frames?
You need two frames to say something about motion in a plane, and you need at least three points to say something about motion in all three dimensions. Right, that should've been three frames, and four points :S Sorry. 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] About MD
On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. 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] g_analyze doubt
On 26/09/2011 4:51 PM, aiswarya pawar wrote: Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. I don't understand your question. Your first sentence implies you know what quantity you want to autocorrelate, and the second implies you don't. g_analyze needs a time series in an .xvg file of some data to compute an autocorrelation. Usually, an .xvg file written by a GROMACS tool is already prepared for such further analysis. 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] g_analyze doubt
HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Thanks, On Mon, Sep 26, 2011 at 12:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/09/2011 4:51 PM, aiswarya pawar wrote: Hi users, I have data with the time frame and the distances, how will compute the autocorrelation of this. i did g_analyze but still dont understand what should be the y axis data when providing input for g_analyze. please help. I don't understand your question. Your first sentence implies you know what quantity you want to autocorrelate, and the second implies you don't. g_analyze needs a time series in an .xvg file of some data to compute an autocorrelation. Usually, an .xvg file written by a GROMACS tool is already prepared for such further analysis. 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] g_analyze doubt
On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? 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
[gmx-users] -shell option of g_hbond
Dear users how can I use -shell option with g_hbond command? I wish to find h-bonds around a particular atom in a definite distance. how can I introduce the index file and cut off distance to it? regards sajad -- 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] About MD
Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? 2011/9/26 Mark Abraham mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. 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] About MD
On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? You are drawing some artificial distinction whose purpose I do not understand. A short simulation on a FES at a temperature low enough that the barriers are larger than the readily available KE will be kinetically trapped. I'd guess that most MD simulations that have ever been run have suffered from this defect. The shape of the FES will generally vary with temperature also. Mark 2011/9/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all, A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] About MD
Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. So I just wonder to know by using MD simulations, the results I obtained is driven by kinetics or thermodynamics. Silly question. XJ 2011/9/26 Mark Abraham mark.abra...@anu.edu.au On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? You are drawing some artificial distinction whose purpose I do not understand. A short simulation on a FES at a temperature low enough that the barriers are larger than the readily available KE will be kinetically trapped. I'd guess that most MD simulations that have ever been run have suffered from this defect. The shape of the FES will generally vary with temperature also. Mark 2011/9/26 Mark Abraham mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. 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 -- 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] About MD
On 26/09/2011 6:25 PM, xiaojing gong wrote: Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. To address this question, I think you need to seek a better description than driven by thermodynamics. All processes are driven by thermodynamics. So I just wonder to know by using MD simulations, the results I obtained is driven by kinetics or thermodynamics. The two growth modes must differ somehow in the conditions that trigger them. For a valid model, which mode you might see will depend what conditions you choose. Mark Silly question. XJ 2011/9/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? I wonder to know how can I set the parameters and in which condition I obtain the structure by thermodynamics, and in which condition (with which parameter setting) I can obtain the structure by kinetics. MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Do you mean that I can obtain the structure by thermodynamics in longer and higher temperature ; obtain the structure by kinetics in shorter and lower temperature? You are drawing some artificial distinction whose purpose I do not understand. A short simulation on a FES at a temperature low enough that the barriers are larger than the readily available KE will be kinetically trapped. I'd guess that most MD simulations that have ever been run have suffered from this defect. The shape of the FES will generally vary with temperature also. Mark 2011/9/26 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all, A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Mapping free-energy surfaces where bonds are not made or broken can be done with conventional MD. Typically, are the structures we find with MD determined mainly by thermodynamics or by kinetics ? MD samples the free-energy surface. Its shape and the temperature determine what structures might be found, and in what proportions. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] BD with Hydrodynamic interactions?
On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] -shell option of g_hbond
On 26/09/2011 5:19 PM, Sajad Ahrari wrote: Dear users how can I use -shell option with g_hbond command? I wish to find h-bonds around a particular atom in a definite distance. how can I introduce the index file and cut off distance to it? See g_hbond -h. You give the radius with -shell and the atom in the group. 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] About MD
On Mon, 26 Sep 2011 09:31:39 +0200 xiaojing gong xnz...@gmail.com wrote: Hi, many thanks for your answer. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e. the structures with the lowest activation barriers)? The energy is NOT minimized in thermodynamics. The relevant quantity that is minimized is the free energy. In NVT-simulations it's the Helmholtz free energy F = E - TS where T is temperature and S the entropy. The minimum of F is obtained in the struggle of minimum energy and maximal entropy. E is, however, minimized when T=0. In NpT you minimize the Gibbs free energy G = E + pV -TS where p is pressure and V is volume. Here to minimize E you would set p=0=T. -- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland Jussi Lehtola, FM Tohtorikoulutettava jussi.leht...@helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -- 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] atomic concentration in x and y axis
Hello, I have done simulations on cyclic peptide nanotubes and trying to calculate the atomic concentration in the x and y axis, to measure the diameter of the tube. I have tried using the g_rdf, but the results are confusing to interpret. Here is the steps which I followed, 1. using trjconv, rotational and translational motions are removed from the centered trajectory. 2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o out.xvg (I understood that the -rdf atom option is the default one and this will calculate the atomic distribution in the x and y plane) I am not sure whether the elimination of translational and rotational motions is enough to calculate this property, should I have to align the structure in the z axis using the PCA analysis? Regards, Raj. -- 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
[Fwd: Re: [gmx-users] BD with Hydrodynamic interactions?]
Forwarded Message From: Sanku M msank...@yahoo.com Reply-to: Sanku M msank...@yahoo.com To: Dommert Florian domm...@icp.uni-stuttgart.de Subject: Re: [gmx-users] BD with Hydrodynamic interactions? Date: Mon, 26 Sep 2011 04:07:38 -0700 (PDT) I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. Please keep correspondence on the mailing list. So how do want to include hydrodynamic interactions into BD ? I think the Lattice-Boltzmann method is a way to do this isn't it ? /Flo From: Dommert Florian domm...@icp.uni-stuttgart.de To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 26, 2011 3:38 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- 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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Dimer simulation problem
Hello again, I centered it and then did the calculation again for minimum image distance but still it showed the same graph as without centering. I tried visualising it using vmd but could not see any such clashes. since I am new to vmd I do not know whether it is possible to calculate such clashes if at all in vmd? I am using dodecahedron box. can it be visualised as it is in vmd? Thank you With regards Kavya On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M hmkv...@gmail.com wrote: Thanks. On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, I was trying to simulate a protein dimer covalently bond with a disulphide bond (230+230 aa long). I used usual protocol as used for simulation of a monomeric protein, using gromacs- 4.5.3, dodecahedron box, tip4p water model and protein to box distance of 1 (-d in editconf). In the middle of the simulation when i checked for minimum image violation there was huge clashes. I am extremely sorry I have been asking regarding this many times but in this it is a dimer and I am not sure what mistake I have done because this happened while simulating another dimer also though not sever. Hence I seek some guidance from this community regarding the problem. I attach the graph herewith. Kindly help. Let me know if I need to give any other information. Please see my post from yesterday for a more detailed reply to this exact same type of question. I am beginning to suspect there's a problem with g_mindist, but I have no solid evidence for that claim, just a hunch. It looks like your protein crosses a periodic boundary and that messes up the calculation. Please center the protein in the box with trjconv -center and re-analyze to see if there are any differences. -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
[gmx-users] VACF
Hello users, I am trying to calculate VACF of cation and anion of [hmim][tf2n] ionic liquid. I am getting some wierd plot which is decaying along the axis. The jpg of this plot has been attached.Please can someone assist me interpret this plot ; I know its simple but am stucked. Thanks, regards. attachment: vachmx.jpg-- 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] Fw: VACF
From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org Date: Mon, 26 Sep 2011 17:27:48 +0530 (GMT+05:30) Subject: VACF Hello users, I am trying to calculate VACF of cation and anion of [hmim][tf2n] ionic liquid. I am getting some wierd plot which is decaying along the axis. Please can someone assist me what does this plot indicate ; I know its simple but am stucked. Thanks, 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: [gmx-users] VACF
On 26/09/2011 9:57 PM, Prema Awati wrote: Hello users, I am trying to calculate VACF of cation and anion of [hmim][tf2n] ionic liquid. I am getting some wierd plot which is decaying along the axis. The jpg of this plot has been attached.Please can someone assist me interpret this plot ; I know its simple but am stucked. The long-time behaviour is not interesting - look at the first picosecond. Also, as manual 8.5.1 hints, if you want to study short-time ACF behaviour, you need to sample data rather more frequently than the relevant time scales. 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
[gmx-users] Re: PCA depends of the number of frames?
Thanks Tsjerk About my question... PCA depend of the number of frames? and your answer: Yes, it does. This has, in fact, been pointed out in the early paperson PCA in MD Please, Would you give me some references, Ricardo Hi Ricardo For the case (1) and (2) the most representative structure was used in the option -s ( One that has the lowest rmsd with respect to the average of each cluster). In case (3) the initial structure of the MD was used in the option -s. If all belong to the same system, it is better to use one referencestructure, to define the conformational space in the same way,allowing direct comparison. When I look the eigenvalues for the case (1) and (2), I found that the eigenvalue is zero only after index=number of frames (see below) In the case (3) the distribution is smooth I could expect a similar distribution for the case (1) and (2), because the frames are representative of the dymanics of the protein. Why this difference? PCA depend of the number of frames? Yes, it does. This has, in fact, been pointed out in the early paperson PCA in MD. I think it's best to read up more about PCA, includingsome introductory material from statistics. One thing I'll give awaythough... ;) Consider the motion of a particle in three dimensions. Ifyou have two frames, you can say something about motion along a line.You need two frames to say something about motion in a plane, and youneed at least three points to say something about motion in all threedimensions. Now in your case, each conformation is one point and theconformational space in which the point moves has 3N dimensions. Ifyou have two points, you can only say something about motion along aline, i.e., you have one component with nonzero eigenvector. Withthree points (conformations), you can obtain two eigenvectors, whichspan a plane, etc. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcherMolecular Dynamics Group* Groningen Institute for Biomolecular Research and Biotechnology* Zernike Institute for Advanced MaterialsUniversity of GroningenThe 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] Re: PCA depends of the number of frames?
On 26/09/2011 10:54 PM, Ricardo Cuya Guizado wrote: Thanks Tsjerk About my question... PCA depend of the number of frames? and your answer: Yes, it does. This has, in fact, been pointed out in the early papers on PCA in MD Please, Would you give me some references, See manual section 8.10 and references, or the references in the literature of work similar to that which you intend to do... Mark Ricardo Hi Ricardo For the case (1) and (2) the most representative structure was used in the option -s ( One that has the lowest rmsd with respect to the average of each cluster). In case (3) the initial structure of the MD was used in the option -s. If all belong to the same system, it is better to use one reference structure, to define the conformational space in the same way, allowing direct comparison. When I look the eigenvalues for the case (1) and (2), I found that the eigenvalue is zero only after index=number of frames (see below) In the case (3) the distribution is smooth I could expect a similar distribution for the case (1) and (2), because the frames are representative of the dymanics of the protein. Why this difference? PCA depend of the number of frames? Yes, it does. This has, in fact, been pointed out in the early papers on PCA in MD. I think it's best to read up more about PCA, including some introductory material from statistics. One thing I'll give away though... ;) Consider the motion of a particle in three dimensions. If you have two frames, you can say something about motion along a line. You need two frames to say something about motion in a plane, and you need at least three points to say something about motion in all three dimensions. Now in your case, each conformation is one point and the conformational space in which the point moves has 3N dimensions. If you have two points, you can only say something about motion along a line, i.e., you have one component with nonzero eigenvector. With three points (conformations), you can obtain two eigenvectors, which span a plane, etc. Hope it helps, 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] atomic concentration in x and y axis
On 26/09/2011 9:04 PM, raj wrote: Hello, I have done simulations on cyclic peptide nanotubes and trying to calculate the atomic concentration in the x and y axis, to measure the diameter of the tube. I have tried using the g_rdf, but the results are confusing to interpret. Here is the steps which I followed, 1. using trjconv, rotational and translational motions are removed from the centered trajectory. 2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o out.xvg (I understood that the -rdf atom option is the default one and this will calculate the atomic distribution in the x and y plane) You need to indicate that you want the 2D analysis with a specific option. Check out g_rdf -h Mark I am not sure whether the elimination of translational and rotational motions is enough to calculate this property, should I have to align the structure in the z axis using the PCA analysis? Regards, Raj. -- 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] Dimer simulation problem
On 26/09/2011 10:02 PM, Kavyashree M wrote: Hello again, I centered it and then did the calculation again for minimum image distance but still it showed the same graph as without centering. Have you followed the kind of workflow suggested here? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions I tried visualising it using vmd but could not see any such clashes. since I am new to vmd I do not know whether it is possible to calculate such clashes if at all in vmd? I am using dodecahedron box. can it be visualised as it is in vmd? Yes, one can be visualized, but some preparation with trjconv -ur compact (as hinted at in trjconv -h) is a good idea. Mark Thank you With regards Kavya On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Thanks. On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, I was trying to simulate a protein dimer covalently bond with a disulphide bond (230+230 aa long). I used usual protocol as used for simulation of a monomeric protein, using gromacs- 4.5.3, dodecahedron box, tip4p water model and protein to box distance of 1 (-d in editconf). In the middle of the simulation when i checked for minimum image violation there was huge clashes. I am extremely sorry I have been asking regarding this many times but in this it is a dimer and I am not sure what mistake I have done because this happened while simulating another dimer also though not sever. Hence I seek some guidance from this community regarding the problem. I attach the graph herewith. Kindly help. Let me know if I need to give any other information. Please see my post from yesterday for a more detailed reply to this exact same type of question. I am beginning to suspect there's a problem with g_mindist, but I have no solid evidence for that claim, just a hunch. It looks like your protein crosses a periodic boundary and that messes up the calculation. Please center the protein in the box with trjconv -center and re-analyze to see if there are any differences. -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 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Dimer simulation problem
Hello again, I centered it and then did the calculation again for minimum image distance but still it showed the same graph as without centering. I tried visualising it using vmd but could not see any such clashes. since I am new to vmd I do not know whether it is possible to calculate such clashes if at all in vmd? I am using dodecahedron box. can it be visualised as it is in vmd? In VMD go to graphics then representations and select periodic. In periodic by clicking on +/- of each axis you can check if your protein bumps into itself. Best, Sarath Thank you With regards Kavya On Wed, Sep 21, 2011 at 5:12 PM, Kavyashree M hmkv...@gmail.com wrote: Thanks. On Wed, Sep 21, 2011 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, I was trying to simulate a protein dimer covalently bond with a disulphide bond (230+230 aa long). I used usual protocol as used for simulation of a monomeric protein, using gromacs- 4.5.3, dodecahedron box, tip4p water model and protein to box distance of 1 (-d in editconf). In the middle of the simulation when i checked for minimum image violation there was huge clashes. I am extremely sorry I have been asking regarding this many times but in this it is a dimer and I am not sure what mistake I have done because this happened while simulating another dimer also though not sever. Hence I seek some guidance from this community regarding the problem. I attach the graph herewith. Kindly help. Let me know if I need to give any other information. Please see my post from yesterday for a more detailed reply to this exact same type of question. I am beginning to suspect there's a problem with g_mindist, but I have no solid evidence for that claim, just a hunch. It looks like your protein crosses a periodic boundary and that messes up the calculation. Please center the protein in the box with trjconv -center and re-analyze to see if there are any differences. -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 Sarath Chandra Dantu Computational Biomolecular Chemistry Max Planck Institute of Biophysical Chemistry Am Fassberg 11, Gottingen 37077 Germany Email: dsar...@gwdg.de Tel: ++49-551-201-2320 Fax: ++49-551-201-2302 -- 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] BD with Hydrodynamic interactions?
I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. From: Sanku M msank...@yahoo.com To: Dommert Florian domm...@icp.uni-stuttgart.de Sent: Monday, September 26, 2011 6:07 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. From: Dommert Florian domm...@icp.uni-stuttgart.de To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 26, 2011 3:38 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658-- 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] BD with Hydrodynamic interactions?
On 26/09/2011 11:59 PM, Sanku M wrote: I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. The manual section of BD doesn't mention it, so very probably not. Mark *From:* Sanku M msank...@yahoo.com *To:* Dommert Florian domm...@icp.uni-stuttgart.de *Sent:* Monday, September 26, 2011 6:07 AM *Subject:* Re: [gmx-users] BD with Hydrodynamic interactions? I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. *From:* Dommert Florian domm...@icp.uni-stuttgart.de *To:* Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, September 26, 2011 3:38 AM *Subject:* Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de mailto:domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- 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] acpype generated different tip3p water paramters
Hi all, I just noted that the tip3p water converted from amber format to gromacs format is [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834 16.0 2 HW 1 WATH1 1 0.4171.00800 3 HW 1 WATH2 1 0.4171.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 0.09572 462750.4 1 3 1 0.09572 462750.4 0.09572 462750.4 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.520836.800 104.520836.800 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif while in amber99sb.ff/tip3p.itp. it is moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW 1 SOL OW 1 -0.83416.0 2 HW 1 SOL HW1 1 0.417 1.00800 3 HW 1 SOL HW2 1 0.417 1.00800 #ifndef FLEXIBLE [ settles ] ; OWfunct doh dhh 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #else [ bonds ] ; i j funct length force_constant 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force_constant 2 1 3 1 104.52 628.02 104.52 628.02 #endif So it seems that the force_constants for O-H bond and H-O-H angle are different? Does this mean amber and gromacs use different parameters for tip3p water? or it's just acpype is not working right? 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] Center of mass: distance restrain for groups
Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membrane. Any ideas please? Thank you very much for your help. Best, Hualin-- 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] Center of mass: distance restrain for groups
Li, Hualin wrote: Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membrane. Any ideas please? Thank you very much for your help. Use the pull code. Distance restraints cannot be applied between different molecules. -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] g_analyze doubt
Mark, i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input? Thanks, On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? 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
[gmx-users] Pressure estimation from NVT
Hi I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure predictions are? e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141 water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics. thanks sikandar -- 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] Center of mass: distance restrain for groups
Hi, Justin, Thank you very much for your reply. I want to use the the pull code like this to do the restrain: pullumbrella pull_geometry distance pull_dimY Y Y ;# 3D pull_start yes ;# add COM distance to initial value (initial value = equilibrium value) pull_ngroups1 ;# excluding the reference pull_group0 DPPC ;# the reference group - the membrane pull_weights0 0 ;# use mass as weight pull_pbcatom0 0 ;# or -1 - important for PBC of groups larger than half box, ;# as here for membrane (see manual) pull_group1 Protein ;# the protein pull_weights1 0 ;# use mass as weight pull_pbcatom1 0 ;# here is no issue since protein is smaller than half the box pull_rate1 0 ;# do not pull, just maintain distance! pull_k1 50 ;# kJ mol^(-1) nm^(-2) However, I am sure about the word pullumbrella, is this command used in free energy calculation to do the sampling ? I am not doing the free energy calculation, should I change something in the mdp file to modify it please? Thanks, Hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 12:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups Li, Hualin wrote: Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membrane. Any ideas please? Thank you very much for your help. Use the pull code. Distance restraints cannot be applied between different molecules. -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 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] Center of mass: distance restrain for groups
I am sorry about the last post, I mean I am not sure about the word pull umbrella, is this command used in free energy calculation to do the sampling ? I am not doing the free energy calculation, should I change something in the mdp file to modify it please? Thanks, Hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 12:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups Li, Hualin wrote: Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membrane. Any ideas please? Thank you very much for your help. Use the pull code. Distance restraints cannot be applied between different molecules. -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 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] Center of mass: distance restrain for groups
Li, Hualin wrote: I am sorry about the last post, I mean I am not sure about the word pull umbrella, is this command used in free energy calculation to do the sampling ? I am not doing the free energy calculation, should I change something in the mdp file to modify it please? Using pull = geometry simply applies a harmonic potential between the two restrained species. No free energy calculation is done unless you do a full free energy workflow and analyze using g_wham. -Justin Thanks, Hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 12:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups Li, Hualin wrote: Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membrane. Any ideas please? Thank you very much for your help. Use the pull code. Distance restraints cannot be applied between different molecules. -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 -- 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] Center of mass: distance restrain for groups
Justin A. Lemkul wrote: Li, Hualin wrote: I am sorry about the last post, I mean I am not sure about the word pullumbrella, is this command used in free energy calculation to do the sampling ? I am not doing the free energy calculation, should I change something in the mdp file to modify it please? Using pull = geometry simply applies a harmonic potential between the Sorry, that should read pull = umbrella :) -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] simulation with position constraint by a harmonic potential
I am running Gromacs for RNAs, and I got a problem during the simulation: How to perform the simulation with each heavy atom constrained to its initial position by a harmonic potential, E = k(r-r0)^2? -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
Liu, Liang wrote: I am running Gromacs for RNAs, and I got a problem during the simulation: How to perform the simulation with each heavy atom constrained to its initial position by a harmonic potential, E = k(r-r0)^2? What you want are position restraints, not constraints (which are for bonds). pdb2gmx should have generated a posre.itp file for this purpose. -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] simulation with position constraint by a harmonic potential
Liu, Liang wrote: Firstly I want to thank for your reply, yes, it should be position restraint. I don't know how to reply in the thread, actually that was my first post. Therefore I have to ask you here, hope it also work to you. Simply reply to the message. The discussion needs to stay on the list. The members are not private tutors. My question is how to perform a position restraint simulation with the heavy atom constrained to its initial position by a harmonic potential E=k(r-r0)^2, which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? You can adjust the force constant in the posre.itp file. There is no automated way of decreasing or increasing a restraint; independent simulations must be run on the different topologies. -Justin Thanks, and any helps will be highly appreciated. -- Best, Liang Liu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_analyze doubt
What have you tried with g_analyze so far? What was your result? Is it what you expect? If not, why isn't it what you expect? Trying something out is far faster and you learn more than waiting for a response from others that don't know exactly what you are doing. At a first look, the command you want to run is g_analyze -f data.xvg -ac autocorr.xvg as you have a data file with time (x) and variable (y) data and you want the autocorrelation function of the variable data. Have you tried that command? 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 aiswarya pawar Sent: Tuesday, 27 September 2011 3:11 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_analyze doubt Mark, i read the help but i still didnt understand how do i compute the time series for this data, should i use this data as such for the input? Thanks, On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.aumailto:mark.abra...@anu.edu.au wrote: On 26/09/2011 5:10 PM, aiswarya pawar wrote: HI Mark, i have a .xvg data for the distance of two atoms in each time frame. 0.00e+00 7.191033e-01 1.00e+00 7.304224e-01 2.00e+00 8.983867e-01 3.00e+00 8.779736e-01 4.00e+00 8.236583e-01 5.00e+00 8.298320e-01 6.00e+00 7.703011e-01 7.00e+00 8.569826e-01 8.00e+00 7.428180e-01 9.00e+00 7.487683e-01 1.00e+01 8.106729e-01 1.10e+01 8.702058e-01 1.20e+01 8.823072e-01 1.30e+01 8.902194e-01 1.40e+01 6.122664e-01 1.50e+01 5.804662e-01 1.60e+01 6.207849e-01 1.70e+01 4.852896e-01 1.80e+01 5.297776e-01 1.90e+01 5.432515e-01 2.00e+01 5.888653e-01 2.10e+01 4.620140e-01 Now i want to find the autocorrelation of the time frame. so i should provide this file as such for input in g_analyze ie x as time and y as distance? or are there any criteria for the g_analyze input. Have you read g_analyze -h and tried it out? Mark -- gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto: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] simulation with position constraint by a harmonic potential
Thanks for the information. It looks the pdb2gmx can generate the posre.itp file and what I use is pdb2gmx -ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce. The file shows: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 3 1 1000 1000 1000 6 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 14 1 1000 1000 1000 15 1 1000 1000 1000 16 1 1000 1000 1000 17 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 23 1 1000 1000 1000 24 1 1000 1000 1000 25 1 1000 1000 1000 27 1 1000 1000 1000 29 1 1000 1000 1000 31 1 1000 1000 1000 32 1 1000 1000 1000 33 1 1000 1000 1000 34 1 1000 1000 1000 35 1 1000 1000 1000 36 1 1000 1000 1000 39 1 1000 1000 1000 41 1 1000 1000 1000 42 1 1000 1000 1000 44 1 1000 1000 1000 45 1 1000 1000 1000 47 1 1000 1000 1000 49 1 1000 1000 1000 50 1 1000 1000 1000 51 1 1000 1000 1000 53 1 1000 1000 1000 54 1 1000 1000 1000 55 1 1000 1000 1000 57 1 1000 1000 1000 59 1 1000 1000 1000 61 1 1000 1000 1000 62 1 1000 1000 1000 63 1 1000 1000 1000 64 1 1000 1000 1000 65 1 1000 1000 1000 66 1 1000 1000 1000 69 1 1000 1000 1000 71 1 1000 1000 1000 72 1 1000 1000 1000 74 1 1000 1000 1000 75 1 1000 1000 1000 77 1 1000 1000 1000 78 1 1000 1000 1000 79 1 1000 1000 1000 80 1 1000 1000 1000 81 1 1000 1000 1000 83 1 1000 1000 1000 84 1 1000 1000 1000 87 1 1000 1000 1000 88 1 1000 1000 1000 89 1 1000 1000 1000 91 1 1000 1000 1000 93 1 1000 1000 1000 95 1 1000 1000 1000 96 1 1000 1000 1000 97 1 1000 1000 1000 98 1 1000 1000 1000 99 1 1000 1000 1000 100 1 1000 1000 1000 103 1 1000 1000 1000 105 1 1000 1000 1000 106 1 1000 1000 1000 108 1 1000 1000 1000 109 1 1000 1000 1000 111 1 1000 1000 1000 113 1 1000 1000 1000 114 1 1000 1000 1000 117 1 1000 1000 1000 118 1 1000 1000 1000 119 1 1000 1000 1000 120 1 1000 1000 1000 122 1 1000 1000 1000 124 1 1000 1000 1000 126 1 1000 1000 1000 127 1 1000 1000 1000 128 1 1000 1000 1000 129 1 1000 1000 1000 130 1 1000 1000 1000 131 1 1000 1000 1000 134 1 1000 1000 1000 136 1 1000 1000 1000 137 1 1000 1000 1000 139 1 1000 1000 1000 140 1 1000 1000 1000 142 1 1000 1000 1000 144 1 1000 1000 1000 145 1 1000 1000 1000 146 1 1000 1000 1000 148 1 1000 1000 1000 149 1 1000 1000 1000 150 1 1000 1000 1000 152 1 1000 1000 1000 154 1 1000 1000 1000 156 1 1000 1000 1000 157 1 1000 1000 1000 158 1 1000 1000 1000 159 1 1000 1000 1000 160 1 1000 1000 1000 161 1 1000 1000 1000 164 1 1000 1000 1000 166 1 1000 1000 1000 167 1 1000 1000 1000 169 1 1000 1000 1000 170 1 1000 1000 1000 172 1 1000 1000 1000 174 1 1000 1000 1000 175 1 1000 1000 1000 176 1 1000 1000 1000 178 1 1000 1000 1000 179 1 1000 1000 1000 180 1 1000 1000 1000 182 1 1000 1000 1000 184 1 1000 1000 1000 186 1 1000 1000 1000 187 1 1000 1000 1000 188 1 1000 1000 1000 189 1 1000 1000 1000 190 1 1000 1000 1000 191 1 1000 1000 1000 194 1 1000 1000 1000 196 1 1000 1000 1000 197 1 1000 1000 1000 199 1 1000 1000 1000 200 1 1000 1000 1000 202 1 1000 1000 1000 203 1 1000 1000 1000 204 1 1000 1000 1000 205 1 1000 1000 1000 208 1 1000 1000 1000 209 1 1000 1000 1000 211 1 1000 1000 1000 212 1 1000 1000 1000 213 1 1000 1000 1000 215 1 1000 1000 1000 217 1 1000 1000 1000 219 1 1000 1000 1000 220 1 1000 1000 1000 221 1 1000 1000 1000 222 1 1000
[gmx-users] CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012
CALL FOR PAPERS 2nd International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2012) # March 26-29, 2012, Orlando, FL (USA) http://www.sel.uniroma2.it/Mod4Sim12 # # Papers Due: *** November 15, 2011 *** # Accepted papers will be published in the conference proceedings and archived # in the ACM Digital Library, IEEE Xplorer and IEEE CS Digital Library. # The Symposium is co-sponsored by IEEE. # The workshop aims to bring together experts in model-based, model-driven and software engineering with experts in simulation methods and simulation practitioners, with the objective to advance the state of the art in model-driven simulation engineering. Model-driven engineering approaches provide considerable advantages to software systems engineering activities through the provision of consistent and coherent models at different abstraction levels. As these models are in a machine readable form, model-driven engineering approaches can also support the exploitation of computing capabilities for model reuse, programming code generation, and model checking, for example. The definition of a simulation model, its software implementation and its execution platform form what is known as simulation engineering. As simulation systems are mainly based on software, these systems can similarly benefit from model-driven approaches to support automatic software generation, enhance software quality, and reduce costs, development effort and time-to-market. Similarly to systems and software engineering, simulation engineering can exploit the capabilities of model-driven approaches by increasing the abstraction level in simulation model specifications and by automating the derivation of simulator code. Further advantages can be gained by using modeling languages, such as UML and SysML – but not exclusively those. For example, modeling languages can be used for descriptive modeling (to describe the system to be simulated), for analytical modeling (to specify analytically the simulation of the same system), and for implementation modeling (to define the respective simulator). A partial list of topics of interest includes: * model-driven simulation engineering processes * requirements modeling for simulation * domain specific languages for modeling and simulation * model transformations for simulation model building * model transformations for simulation model implementation * model-driven engineering of distributed simulation systems * relationship between metamodeling standards (e.g., MOF, Ecore) and distributed simulation standards (e.g., HLA, DIS) * metamodels for simulation reuse and interoperability * model-driven technologies for different simulation paradigms (discrete event simulation, multi-agent simulation, sketch-based * simulation, etc.) * model-driven methods and tools for performance engineering of simulation systems * simulation tools for model-driven software performance engineering * model-driven technologies for simulation verification and validation * model-driven technologies for data collection and analysis * model-driven technologies for simulation visualization * Executable UML * Executable Architectures * SysML / Modelica integration * Simulation Model Portability and reuse * model-based systems verification and validation * simulation for model-based systems engineering To stimulate creativity, however, the workshop maintains a wider scope and welcomes contributions offering original perspectives on model-driven engineering of simulation systems. +++ On-Line Submissions and Publication +++ We invite paper submissions in three forms: 1. Full paper (max 8 pages), describing innovative research results. These papers are eligible for the best paper award and may be invited for an extended version in a special issue of the SCS SIMULATION journal. 2. Work-in-progress paper (max 6 pages), describing novel research ideas and promising work that have not yet been fully evaluated. 3. Short paper (max 6 pages), describing industrial and hands-on experience on any relevant area (i.e. military, government, space, etc.). All the papers must be submitted through the SCS conference management systems (http://www.softconf.com/scs/DEVS12/), selecting the Mod4Sim track in the Submission Categories section. All the submitted papers must be in PDF format and must conform to the
RE: [gmx-users] VACF
You must have a different plot to what you sent then, as that graph shows no decay what so ever, it appears to be essentially constant. What that means is on that time scale there is no correlation between the velocity at a point in time and any time on the x axis before/previously. 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 Prema Awati Sent: Monday, 26 September 2011 9:58 PM To: gmx-users@gromacs.org Subject: [gmx-users] VACF Hello users, I am trying to calculate VACF of cation and anion of [hmim][tf2n] ionic liquid. I am getting some wierd plot which is decaying along the axis. The jpg of this plot has been attached.Please can someone assist me interpret this plot ; I know its simple but am stucked. Thanks, 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: [gmx-users] Pressure estimation from NVT
Have you looked at the data from which you calculated the pressure average from? 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 Sikandar Mashayak Sent: Tuesday, 27 September 2011 3:48 AM To: Discussion list for GROMACS users Subject: [gmx-users] Pressure estimation from NVT Hi I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure predictions are? e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141 water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics. thanks sikandar -- 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] simulation with position constraint by a harmonic potential
Liu, Liang wrote: Thanks for the information. It looks the pdb2gmx can generate the posre.itp file and what I use is pdb2gmx -ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce. The file shows: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 snip It is unnecessary to paste this information. So how to adjust the force constraint to the harmonic poteitial E = k(r-r0)^2, with different values of k? The file format is discussed in the manual, Chapter 4. You can alter the force constants in x, y, and z dimensions independently. The force constants are listed in the fx, fy, and fz columns. I am totally a new user of Gromacs, even MD simulation. Please help, I would suggest you familiarize yourself with Gromacs capabilities, file formats, and workflows by working through any of the multitude of tutorials linked on the Gromacs website. -Justin Thanks a lot. On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Firstly I want to thank for your reply, yes, it should be position restraint. I don't know how to reply in the thread, actually that was my first post. Therefore I have to ask you here, hope it also work to you. Simply reply to the message. The discussion needs to stay on the list. The members are not private tutors. My question is how to perform a position restraint simulation with the heavy atom constrained to its initial position by a harmonic potential E=k(r-r0)^2, which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? You can adjust the force constant in the posre.itp file. There is no automated way of decreasing or increasing a restraint; independent simulations must be run on the different topologies. -Justin Thanks, and any helps will be highly appreciated. -- Best, Liang Liu -- ==__== 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- Best, Liang Liu -- 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] Pressure estimation from NVT
Dallas Warren wrote: Have you looked at the data from which you calculated the pressure average from? Very important point. There was a bug in pressure-related output in Gromacs versions up to, and including 4.5.3. The instantaneous values are correct, but the averages are flawed. -Justin 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 *Sikandar Mashayak *Sent:* Tuesday, 27 September 2011 3:48 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Pressure estimation from NVT Hi I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure predictions are? e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141 water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics. thanks sikandar -- 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] Pressure estimation from NVT
On 27/09/2011 3:48 AM, Sikandar Mashayak wrote: Hi I am trying to determine pressure of water at given density and temperature using SPC/E water model. To achieve this, I am doing NVT bulk simulations and then using g_energy I get average pressure values. The question I have is how accurate these average pressure predictions are? e.g. I get average pressure of 185 bar for 300 K and 1 g/cm^3 water density, but theoretical value for it is around 1 bar. What are the possible reasons for this much deviation from theoretical value? Is there anything wrong with my set up? I am using 2141 water molecules in 4*4*4 periodic box, Nose-Hoover thermostat with 0.2ps time constant , MD algorithm with 1fs time-step, LJ with 1.5 nm cut off and PME for electrostatics. The length of your simulation, and the absence of the equilibration period from your data collection are also critical factors in obtaining accurate converged averages, but usually neglected when people report what might be anomalies... please see http://www.gromacs.org/Documentation/Terminology/Pressure 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] simulation with position constraint by a harmonic potential
Thanks. Is this position restraint same to the one Position Restrained MD. I see some tutorial shows there are always three step to perform a simulation: Energy minimization, Position Restrained MD and MD Simulation. Is it possible to fulfill the position restraint during Position Restrained MD? Thanks. On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu, Liang wrote: Firstly I want to thank for your reply, yes, it should be position restraint. I don't know how to reply in the thread, actually that was my first post. Therefore I have to ask you here, hope it also work to you. Simply reply to the message. The discussion needs to stay on the list. The members are not private tutors. My question is how to perform a position restraint simulation with the heavy atom constrained to its initial position by a harmonic potential E=k(r-r0)^2, which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? You can adjust the force constant in the posre.itp file. There is no automated way of decreasing or increasing a restraint; independent simulations must be run on the different topologies. -Justin Thanks, and any helps will be highly appreciated. -- Best, Liang Liu -- ==**== 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 ==**== -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
On 27/09/2011 12:49 PM, Liu, Liang wrote: Thanks. Is this position restraint same to the one Position Restrained MD. I see some tutorial shows there are always three step to perform a simulation: Energy minimization, Position Restrained MD and MD Simulation. Always is too strong, but this is common. Is it possible to fulfill the position restraint during Position Restrained MD? Thanks. Yes, hence the name. How well they can be fulfilled depends on the initial and simulation conditions. Mark On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Liu, Liang wrote: Firstly I want to thank for your reply, yes, it should be position restraint. I don't know how to reply in the thread, actually that was my first post. Therefore I have to ask you here, hope it also work to you. Simply reply to the message. The discussion needs to stay on the list. The members are not private tutors. My question is how to perform a position restraint simulation with the heavy atom constrained to its initial position by a harmonic potential E=k(r-r0)^2, which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? You can adjust the force constant in the posre.itp file. There is no automated way of decreasing or increasing a restraint; independent simulations must be run on the different topologies. -Justin Thanks, and any helps will be highly appreciated. -- Best, Liang Liu -- 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 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Best, Liang Liu -- 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
