[gmx-users] umbrella sampling with position restraint
Hi gmx users I am using umbrella sampling method for calculate the PMF for one molecule in a bilayer system made of SDS and decanol. when the molecule is in the middle of the bilayer, generate a hole and the bilayer system is lost. I am thinking use position restraint for one of the atoms in the SDS (sodium dodecyl sulfate). is this a good idea? any suggestion will be well received Thanks in advance Víctor E. Bahamonde Padilla Laboratorio de Fisicoquímica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl -- 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] Converting between cartesian coordinates and torsion angles
Hi, As far as I understand, a topology (a .top file) and a conformation (e.g., a .gro file) contain enough information to calculate the torsion angles of that specific conformation. Table 5.5 (page 124) in the GROMACS manual[1] describes possible interactions (which are contained in the topology) between different molecules while the conformation contains the cartesian coordinates. I did not immediately find a way to convert between the cartesian coordinates and the torsion angles. Can GROMACS do it or do I need to understand (or just find) all the functions/formulas that are referenced in Table 5.5? I have included screenshots of Table 5.5[2] and the relevant part of some example .top file[3]. (Also, it seems that I can use the read_tpx method defined in include/tpxio.h to read in a topology from a .tpr file. This would then, after converting the cartesian coordinates of some conformation, enable me to work with the torsion angles in my own program before writing cartesian coordinates back for use with GROMACS.) Regards, Martin. [1] http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf [2] http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png [3] http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png -- 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] water hydration map analysis help
Dear all I would like to analysis the hydration site near the proteins the one done by the following paper Biophysical Journal Volume 79 December 2000 2966–2974 I would like to do the analysis the trajectory like this.is there any tool available in gromacs to do this kind of analysis could anyone help me in this regard. what tool will be useful to analysis this kind of results. Regards E R Azhagiya singam -- 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] GridCount
Dear all I would like to analysis the hydration site near the proteins the one done by the following paper Biophysical Journal Volume 79 December 2000 2966–2974 I would like to do the analysis the trajectory like this. is this possible to do with GridCound tool if it is possible please explain the steps involved Regards E R Azhagiya singam -- 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] Converting between cartesian coordinates and torsion angles
On 13/11/2010 12:49 AM, Martin Kamp Jensen wrote: Hi, As far as I understand, a topology (a .top file) and a conformation (e.g., a .gro file) contain enough information to calculate the torsion angles of that specific conformation. Table 5.5 (page 124) in the GROMACS manual[1] describes possible interactions (which are contained in the topology) between different molecules while the conformation contains the cartesian coordinates. I did not immediately find a way to convert between the cartesian coordinates and the torsion angles. Can GROMACS do it or do I need to understand (or just find) all the functions/formulas that are referenced in Table 5.5? Section 4.2 has the relevant definitions. Table 5.5 pertains to the definition of force field elements that act upon (for example) such internal coordinates, which is not what you're looking for. I have included screenshots of Table 5.5[2] and the relevant part of some example .top file[3]. (Also, it seems that I can use the read_tpx method defined in include/tpxio.h to read in a topology from a .tpr file. This would then, after converting the cartesian coordinates of some conformation, enable me to work with the torsion angles in my own program before writing cartesian coordinates back for use with GROMACS.) Either a) write something that post-processes the result of grompp -pp in concert with the same coordinate file to get the internal coordinates, or b) use a hacked version of mdrun that writes internal coordinates from within src/gmxlib/bondfree.c (probably used as mdrun -rerun) to create input for your procedure. Mark Regards, Martin. [1] http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf [2] http://imada.sdu.dk/~mkjens04/gromacs/intra-molecular_interactions_definitions.png http://imada.sdu.dk/%7Emkjens04/gromacs/intra-molecular_interactions_definitions.png [3] http://imada.sdu.dk/~mkjens04/gromacs/part_of_top_file.png http://imada.sdu.dk/%7Emkjens04/gromacs/part_of_top_file.png -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_densmap options and use
Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Thank you for your help and your guidance Stefane -- 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_densmap options and use
On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. 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] PGI link error: unknown switch --rpath attempted static link of dynamic object fftw/lib/libfftw3.so
Mark Abraham wrote, On 12/11/2010 17:02: On 13/11/2010 3:15 AM, Yudong Sun wrote: Hi, I have some troubles when compiling GROMACS 4.5.3 using PGI compiler on the -rpath flag and also a static link to dynamic libfftw3.so. I use the pre-installed FFTW 3.2.2.1 library on my Linux system. The FFTW library is managed by the Modules package. The fftw module automatically sets the environ variable as: FFTW_POST_LINK_OPTS = -L/opt/fftw/3.2.2.1/lib -Wl,-rpath=/opt/fftw/3.2.2.1/lib -lfftw3 -lfftw3f So how does configure use this information? (hint: providing the configure command line is essential for us to understand any context!) When compiling, an error occurs on the -rpath: pgcc -fast -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /opt/fftw/3.2.2.1/lib/libfftw3.so /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -ldl -lnsl -lm --rpath /opt/fftw/3.2.2.1/lib --rpath /opt/fftw/3.2.2.1/lib pgcc-Error-Unknown switch: --rpath pgcc-Error-Unknown switch: --rpath Pgcc doesn't recognize --rpath. The correct format is a single dash only -rpath. Sounds like configure isn't handling pgcc properly. However, GROMACS is using very vanilla autoconf stuff, so I'm strongly of the opinion that the problem isn't on the GROMACS side. If I manually remove the extra '-' (-rpath /opt/fftw/3.2.2.1/lib) and rerun the command line, a link error appears: /usr/bin/ld: attempted static link of dynamic object `/opt/fftw/3.2.2.1/lib/libfftw3.so' The command line links the dynamic fftw library. As the 'configure --help' shows the default is a static build. Why doesn't the configure pick the libfftw3.a but the libfftw3.so? The fftw library on my system contains both static and dynamic libraries. Don't know. Ask the autoconf list. I have also tried to make the old GROMACS 4.0.7 which has shown the same problems as above. Any workarounds to the problems or what options should I pass to the configure? Don't bother with PGI compilers. GROMACS performance is 99% compiler-independent, thanks to hand-coded assembly for the inner loops. Use gcc. I have tried GCC. It has the same static link problem: attempted static link of dynamic object `/opt/fftw/3.2.2.1/lib/libfftw3.so' Yudong Mark The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses by Star. The service is powered by MessageLabs. -- 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: gmx-users Digest, Vol 79, Issue 88
On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? Yes I have read the help of the tool but it is not clear to me why i have to choose three groups since i want to compute the water density map around my peptides (- two groups) I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. I don't understand your response since with the above command and -o argument show that an xpm with the name 6_Peptide_53A6_densmap.xpm should appear :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /work/taulier01/gromacs-4.5.3/bin/g_densmap_mpi (-: Option Filename Type Description -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s ./TRAJ/TPR/em.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od 6_Peptide_53A6_densmap.dat Output, Opt! Generic data file -o 6_Peptide_53A6_densmap.xpm Output X PixMap compatible matrix file Stefane 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
[gmx-users] umbrella sampling with position restraint
Dear Víctor: what you should do depends on what you want to get. I suggest that you simply cut your PMF at the point where the bilayer is lost and explain why it is cut. If you really want to pursue your idea, then you need to have a good grasp of exactly what you are doing by such a method. You would want to start by calculating the free energy of applying this additional restraint to a bilayer that is not interacting with your solute. The problem then is that you would really need to also calculate the free energy of releasing this restraint upon reaching the center of the bilayer, and it sounds like that not only unfeasible, but also uninstructive. My last thought is that you'll want to ensure that the destruction of the bilayer is actually the equilibrium action of your solute. Perhaps you simply don't have the equilibrated orientation, etc, that would allow this system to be stable. In that case, you might consider using your method as a way to generate the starting structure, which would then be simulated in the absence of this additional restraint for data collection. In the end, you need to have a clear idea of what you want the PMF for and also have a clear idea of your path fro the unrestrained state to your umbrellas. Free energy is a state property, but you need to understand the full path, and if you forget to include the cost of something like adding the additional restraint to a neat bilayer, then your study will be of little value. Note that the relative free energies in the state with the additional restraints are not useful in and of themselves just as the intermediates of any alchemical transformation are not useful on their own and are only useful as a means to get to the endpoint. Chris. -- original message -- I am using umbrella sampling method for calculate the PMF for one molecule in a bilayer system made of SDS and decanol. when the molecule is in the middle of the bilayer, generate a hole and the bilayer system is lost. I am thinking use position restraint for one of the atoms in the SDS (sodium dodecyl sulfate). is this a good idea? any suggestion will be well received Thanks in advance Víctor E. Bahamonde Padilla Laboratorio de Fisicoquímica Molecular Departamento de Química Facultad de Ciencias Universidad de Chile Phone: 562-978-7443 vedua...@ug.uchile.cl -- 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_densmap options and use
sa wrote: On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? Yes I have read the help of the tool but it is not clear to me why i have to choose three groups since i want to compute the water density map around my peptides (- two groups) The first two groups determine the axis. Per g_densmap -h: Three groups should be supplied, the centers of mass of the first two groups define the axis, the third defines the analysis group. I suspect the fact that you've chosen SOL for the second group might be causing problems (since, presumably, you have water all around), but I have never used g_densmap, so I don't know for sure. -Justin I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. I don't understand your response since with the above command and -o argument show that an xpm with the name 6_Peptide_53A6_densmap.xpm should appear :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /work/taulier01/gromacs-4.5.3/bin/g_densmap_mpi (-: Option Filename Type Description -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s ./TRAJ/TPR/em.tpr
Re: [gmx-users] PGI link error: unknown switch --rpath attempted static link of dynamic object fftw/lib/libfftw3.so
Little bit more background/context would help. Do you try to compile an all static library? If so you of course need a static library of fftw. If it is not all static it normally should accept the dynamic fftw. Then please give us the full configure line, the gcc command line of the link step and the full error message. Roland On Fri, Nov 12, 2010 at 12:17 PM, Yudong Sun yud...@nag.co.uk wrote: Mark Abraham wrote, On 12/11/2010 17:02: On 13/11/2010 3:15 AM, Yudong Sun wrote: Hi, I have some troubles when compiling GROMACS 4.5.3 using PGI compiler on the -rpath flag and also a static link to dynamic libfftw3.so. I use the pre-installed FFTW 3.2.2.1 library on my Linux system. The FFTW library is managed by the Modules package. The fftw module automatically sets the environ variable as: FFTW_POST_LINK_OPTS = -L/opt/fftw/3.2.2.1/lib -Wl,-rpath=/opt/fftw/3.2.2.1/lib -lfftw3 -lfftw3f So how does configure use this information? (hint: providing the configure command line is essential for us to understand any context!) When compiling, an error occurs on the -rpath: pgcc -fast -o grompp grompp.o ./.libs/libgmxpreprocess_mpi_d.a /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/mdlib/.libs/libmd_mpi_d.a ../mdlib/.libs/libmd_mpi_d.a /opt/fftw/3.2.2.1/lib/libfftw3.so /usr/local/packages/nag/GROMACS/gromacs-4.5.3/src/gmxlib/.libs/libgmx_mpi_d.a ../gmxlib/.libs/libgmx_mpi_d.a -ldl -lnsl -lm --rpath /opt/fftw/3.2.2.1/lib --rpath /opt/fftw/3.2.2.1/lib pgcc-Error-Unknown switch: --rpath pgcc-Error-Unknown switch: --rpath Pgcc doesn't recognize --rpath. The correct format is a single dash only -rpath. Sounds like configure isn't handling pgcc properly. However, GROMACS is using very vanilla autoconf stuff, so I'm strongly of the opinion that the problem isn't on the GROMACS side. If I manually remove the extra '-' (-rpath /opt/fftw/3.2.2.1/lib) and rerun the command line, a link error appears: /usr/bin/ld: attempted static link of dynamic object `/opt/fftw/3.2.2.1/lib/libfftw3.so' The command line links the dynamic fftw library. As the 'configure --help' shows the default is a static build. Why doesn't the configure pick the libfftw3.a but the libfftw3.so? The fftw library on my system contains both static and dynamic libraries. Don't know. Ask the autoconf list. I have also tried to make the old GROMACS 4.0.7 which has shown the same problems as above. Any workarounds to the problems or what options should I pass to the configure? Don't bother with PGI compilers. GROMACS performance is 99% compiler-independent, thanks to hand-coded assembly for the inner loops. Use gcc. I have tried GCC. It has the same static link problem: attempted static link of dynamic object `/opt/fftw/3.2.2.1/lib/libfftw3.so ' Yudong Mark The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is: Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom. This e-mail has been scanned for all viruses by Star. The service is powered by MessageLabs. -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 79, Issue 89
sa wrote: On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? Yes I have read the help of the tool but it is not clear to me why i have to choose three groups since i want to compute the water density map around my peptides (- two groups) The first two groups determine the axis. Per g_densmap -h: Three groups should be supplied, the centers of mass of the first two groups define the axis, the third defines the analysis group. I suspect the fact that you've chosen SOL for the second group might be causing problems (since, presumably, you have water all around), but I have never used g_densmap, so I don't know for sure. -Justin Ok I will try and play with the different groups of my system to see if it works... Stefane I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. I don't understand your response since with the above command and -o argument show that an xpm with the name 6_Peptide_53A6_densmap.xpm should appear :-) G R O M A C S (-: Gnomes, ROck Monsters And Chili Sauce :-) VERSION 4.5.3 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-)
[gmx-users] Probability contact map from g_mdmat
Dear All, I was playing around with g_mdmat to try and obtain a probability contact plot instead of a mean plot or a frame dump, where it would count the number of times a distance would occur between a range eg. 0-0.4nm. This way the map would show the contact, as well as the propensity to form that contact, relative to the covalent bonds shown on the diagonal. Anyway this would be more important to me than a means plot. I have searched the literature and this forum for contact map gromacs keywords without results except for a conversion from xpm to numbers script and a script that returns the various contacts g_mdmat found. Hence, I wanted to know if someone has done this on their own, so I won't reinvent. If not, I will modify the source and upload it to the user contribution page. Let me know. Cordially, Ali -- 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_densmap options and use
On 13/11/2010 4:58 AM, sa wrote: On 13/11/2010 4:07 AM, sa wrote: Dear All, I would like to compute the average 2D density distribution of the water around 6 peptides aggregated in the cluster within the simulation box with gromacs, for that I think that g_densmap is the the good tool (correct ?). However it is not very clear for how to use g_densmap. Below the command I used with g_densmap (ver GMX 4.5.3) g_densmap_mpi -f ./TRAJ/XTC/6_Pep_Urea_Pref_All.xtc -s ./TRAJ/TPR/em.tpr -bin 0.02 -amax 30 -rmax 30 -b 0 -e 8 -o 6_Peptide_53A6_densmap.xpm -od 6_Peptide_53A6_densmap.dat When I use the above command, g_densmap asks me to choose two groups to define the axis and an analysis group: Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Reading file ./TRAJ/TPR/em.tpr, VERSION 4.5.1 (single precision) Select two groups to define the axis and an analysis group Group 0 ( System) has 86359 elements Group 1 (Protein) has 546 elements Group 2 ( Protein-H) has 396 elements Group 3 (C-alpha) has48 elements Group 4 ( Backbone) has 144 elements Group 5 ( MainChain) has 192 elements Group 6 ( MainChain+Cb) has 234 elements Group 7 (MainChain+H) has 246 elements Group 8 ( SideChain) has 300 elements Group 9 (SideChain-H) has 204 elements Group10 (Prot-Masses) has 546 elements Group11 (non-Protein) has 85813 elements Group12 ( Other) has 17320 elements Group13 (URE) has 17320 elements Group14 ( CL) has 6 elements Group15 ( Water) has 68487 elements Group16 (SOL) has 68487 elements Group17 ( non-Water) has 17872 elements Group18 (Ion) has 6 elements Group19 (URE) has 17320 elements Group20 ( CL) has 6 elements Group21 ( Water_and_ions) has 68493 elements Select a group: 1 Selected 1: 'Protein' Select a group: 16 Selected 16: 'SOL' Select a group: 16 Selected 16: 'SOL' I chose protein and SOL, the program ask me to choose a third group (?) What to choose ? Doesn't g_densmap -h explain the three groups? Yes I have read the help of the tool but it is not clear to me why i have to choose three groups since i want to compute the water density map around my peptides (- two groups) You need to define an axis by the line between the centers of mass of two groups. Almost surely the COM of your protein cluster and the COM of your water is a random line. I don't know what there is about your system that makes you want a 2D density distribution, but if there is, you need to come up with a sensible axis around which to compute. Only then does the distribution of third group get computed. I choose SOL again, the program computes something but i can not inspect the results are what i want since no xpm is generated by g_densmap (is this a bug ?) Probably badly-formed input is silently breaking something somewhere. I don't understand your response since with the above command and -o argument show that an xpm with the name 6_Peptide_53A6_densmap.xpm should appear Agreed, but lets get your input formed sensibly before deducing that there's a bug or anything. I had a quick look at the code, and Peter Kasson designed it so that if you use -od then you won't get the -o output. You could get both from two invocations of g_densmap, which doesn't sound like a good design, and certainly contradicts the documentation. For the moment, I'll fix the documentation. 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] Probability contact map from g_mdmat
On 13/11/2010 6:30 AM, Ali Naqvi wrote: Dear All, I was playing around with g_mdmat to try and obtain a probability contact plot instead of a mean plot or a frame dump, where it would count the number of times a distance would occur between a range eg. 0-0.4nm. This way the map would show the contact, as well as the propensity to form that contact, relative to the covalent bonds shown on the diagonal. Anyway this would be more important to me than a means plot. I have searched the literature and this forum for contact map gromacs keywords without results except for a conversion from xpm to numbers script and a script that returns the various contacts g_mdmat found. Hence, I wanted to know if someone has done this on their own, so I won't reinvent. If not, I will modify the source and upload it to the user contribution page. Let me know. Do be sure that you can't get what you want from cunning use of some of the other tools, e.g. g_bond, g_dist or g_mindist. 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] GFP chromophore topology help
Thank you for the help. I have successfully constructed the chromphore molecule but still have problem in connecting it to the neigbhouring residues. I don't know how the connection sequence needs to be given in gromacs. Please help with regards, Rama On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Dear gromacs users: I have constructed the Amber03 force fields parameters (bonds,angles, proper and imporer dihedral.) for the chromophore (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the topology. But after energy minimization of the system, the conformation of the chromophore totally changed and the benzene and imidazole ring got puckered although i did not got any error message. No Gromacs tool will check your work for you. It will do what you tell it. Likely you omitted some necessary bonded parameters (bonds, angles, impropers, etc). Either that, or the parameters you supplied produce the incorrect behavior. -Justin Could anyone help me? Thank you. with regards, Rama -- 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 list gmx-us...@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 -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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] GFP chromophore topology help
Thank you for the help. I have successfully constructed the chromphore molecule but still have problem in connecting it to the neigbhouring residues. I don't know how the connection sequence needs to be given in gromacs. Please help with regards, Rama On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Dear gromacs users: I have constructed the Amber03 force fields parameters (bonds,angles, proper and imporer dihedral.) for the chromophore (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the topology. But after energy minimization of the system, the conformation of the chromophore totally changed and the benzene and imidazole ring got puckered although i did not got any error message. No Gromacs tool will check your work for you. It will do what you tell it. Likely you omitted some necessary bonded parameters (bonds, angles, impropers, etc). Either that, or the parameters you supplied produce the incorrect behavior. -Justin Could anyone help me? Thank you. with regards, Rama -- 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 list gmx-us...@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 -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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] GFP chromophore topology help
Ramachandran G wrote: Thank you for the help. I have successfully constructed the chromphore molecule but still have problem in connecting it to the neigbhouring residues. I don't know how the connection sequence needs to be given in gromacs. Please help You stand a much better chance of getting useful help if you at least describe what you attempted and why it didn't work. For the GFP chromophore, which incorporates into the backbone, you need to add connectivity in the .rtp file like any other amino acid residue (-C and +N), and define the residue as Protein in residuetypes.dat (if using version 4.5.x). Without knowing what you've done, though, I'm only guessing. -Justin with regards, Rama On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Dear gromacs users: I have constructed the Amber03 force fields parameters (bonds,angles, proper and imporer dihedral.) for the chromophore (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the topology. But after energy minimization of the system, the conformation of the chromophore totally changed and the benzene and imidazole ring got puckered although i did not got any error message. No Gromacs tool will check your work for you. It will do what you tell it. Likely you omitted some necessary bonded parameters (bonds, angles, impropers, etc). Either that, or the parameters you supplied produce the incorrect behavior. -Justin Could anyone help me? Thank you. with regards, Rama -- 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] on calculation of the atomic covariance
Dear Tsjerk, Thanks very much. Yes, true, difference in the ranges of the covariances means there is difference between the two systems. I did try the modified g_covar in the contribution section but couldn't make it work first, but I realized it worked only for GROMACS ver 3.3.3. Now, I am able to calculate the correlation matrix. Thanks very much for all your help and pointers. Sincerely, Vignesh On Thu, Nov 11, 2010 at 4:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vignesh, If your covariances show different ranges, isn't that a difference between your systems, wild-type and mutated? Then again, there's also noise in the covariances (noise in the fluctuations, ergo noise in the noise ;)). The rest might be comparable, making scaling based on the extremes seem like a bad idea. You might be better of calculating correlations, rather than covariances. There's a modified g_covar in the contributions section of the gromacs site for calculating those. Cheers, Tsjerk On Thu, Nov 11, 2010 at 3:53 AM, Vigneshwar Ramakrishnan vmsrvign...@gmail.com wrote: Dear All, I tried using the xpm2ps -combine option to plot the two matrices in the same plot. xpm2ps -f covara_cognate.xpm -f2 covara_G5C.xpm -diag none -combine halves -cmin -0.5 -cmax 0.8 However, I still get two legends and each of the matrices are scaled differently. That is, the output range is NOT combined, as the -combine option is supposed to do. I tried different options (add, sub, div ; with and without the -cmin and -cmax options etc) I am sure I am missing something here. May I please know if anybody got it worked, and if so, can help me out? Thanks very much, Vignesh On Thu, Nov 11, 2010 at 10:12 AM, Vigneshwar Ramakrishnan vmsrvign...@gmail.com wrote: Thanks very much, Justin. Somehow this thread did not come up during my search. Really appreciate your help. Sincerely, Vignesh On Wed, Nov 10, 2010 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: There are two relevant threads on this same topic that will likely provide some insight (particularly the second): http://lists.gromacs.org/pipermail/gmx-users/2009-November/046846.html http://lists.gromacs.org/pipermail/gmx-users/2009-November/046854.html -Justin Vigneshwar Ramakrishnan wrote: Dear All, I am trying to study the effect of single-point mutations on correlated motions in a protein-DNA system. I am able to calculate the atomic covariance matrix using the g_covar -xpma option. However, when I try to compare the covariance matrices for the two systems (to study the effect of the mutation), I find that the output is not scaled identically. That is, in one of the systems the atomic covariance varies between -0.04 and +0.5 whereas in the other it varies between -0.1 and +0.4. Now, this means that I cannot compare the two systems immediately from the eps file output (obtained after xpm2ps). Could anybody please tell me if there is a way to plot the output on identical scales (say, -1 to +1, or any other scale) using GROMACS? The other way, I understand is to use the ascii output of g_covar and use the values to create the covariance plot using softwares like MATLAB which can rescale the image colors. However, for this, one needs to calculate the atomic covariance from the ascii output (which is x1x1,x1y1,x1z1 etc). From the manual, I understand that the way to calculate atomic covariance is for each atom pair the sum of the xx, yy and zz covariances. Am I right if I understand that this means: atomic cov (X1) = x1x1 + y1y1 + z1z1 atomic cov (X2) = x2x2 + y2y2 + z2z2 ... I greatly appreciate any help or pointers. Thanks very much, Sincerely, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of Singapore, Singapore Strive for Excellence, Never be satisfied with the second Best!! I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) -- 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 -- R.Vigneshwar Graduate Student, Dept. of Chemical Biomolecular Engg, National University of
[gmx-users] Molecular dynamics hydration site
Dear all http://www.sciencedirect.com/science?_ob=MImg_imagekey=B94RW-4TYB1FX-K-1_cdi=56421_user=1245000_pii=S0006349500765337_coverDate=12/31/2000_sk=%23TOC%2356421%232000%23999209993%23703217%23FLA%23display%23Volume_79,_Issue_6,_Pages_2783-3354_(December_2000)%23tagged%23Volume%23first%3D79%23Issue%23first%3D6%23date%23(December_2000)%23view=c_gw=ywchp=dGLbVlb-zSkWbmd5=4e66a17da4627571bfd990beae45d486ie=/sdarticle.pdf I read the above linked paper about the to find a molecular density hydration map it says For each step of the MD trajectory, the protein was fitted to a consistent frame of reference. I did this by using trjconv i have fitted the protein in my trajectory Next, the same transformation was applied to the water molecule coordinates, taking the periodic boundaries into account. I did the same by using trjconv by using the trajectory i have obtained from the previous step The coordinates of the water oxygen atoms were then mapped onto the three-dimensional rectangular grid with a 0.5 Å grid step, producing an average three-dimensional number density distribution. The particular choice of the grid step is a compromise between the uncertainty in location of the density features and the statistical error in the local density value that arises due to a lower number of counts in each grid cell. At the chosen grid step every cell in the regions corresponding to bulk solvent would have at least 50 counts over the entire trajectory. The density map was smoothed by averaging the value of each cell with six of its nearest neighbors before further manipulations. I did the above step by using GridCount tool i got a grid.dat then i transformed the that to a vmd readable format density map. but when i visualize the file in vmd i got a lot of density over the corner but i was not able to visualize the it near the protein molecule as given in the above mentioned paper could anyone helpme in this regard how to do the same analysis in gromacs. Thanks in advance E R Azhagiya singam -- 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
