[gmx-users] interaction energy
HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface. Enon-bond = E(vdw) + E(elec) gold atoms charge in simulation were considered 0, then E non-bonded=E(vdw) Is this true? The interaction energy is equal to the van der Waals energy? Fatemeh Ramezani -- 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] Plotting data from g_spatial
Dear users I have a question regarding the cube file output we get from g_spatial analysis. My system comprises of hundreds of ionic liquids (composed of cation and anion). If I would like to see the spatial distribution of anions around cation, how do I get an average distribution. E.g, the way I am using it now, spatial distribution of all the anions in simulation box is shown, which is very inconclusive. I cannot specify a particular set of cations and anions, as they separate over time. Please help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] installing gromacs-4.6.1 with CMake
Hi. I'm trying to build a build with cmake-2.8.10.2-linux for 'gromacs-4.6.1' as the build target. First, I extracted gromacs-4.6.1.tar.gz and, create a new folder; build inside the extracted folder. Then, inside build folder, I configured using CMake. $ tar -xvzf gromacs-4.6.1.tar.gz $ cd gromacs-4.6.1 $ mkdir build $ cd build $ cmake .. However, I got an error. -- CMake Error: The source directory /home/okayuka/Gromacs does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. - Inside gromacs-4.6.1 directory, there is certainly CMakeLists.txt. For this, I think cmake mistaking /home/okayuka/Gromacs for /home/okayuka/Gromacs/gromacs-4.6.1 as ' the source directory'. Would you please tell me how correct this mismatch of the source directory? -Yuka -- ＊ 中野佑香 立教大学 理学研究科化学専攻 博士前期課程 1年 理論創薬・分子設計 常盤研究室 〒171-8501 東京都豊島区西池袋3-34-1 4号館4230教室 Email: yuk...@rikkyo.ac.jp 09cc0...@rikkyo.ac.jp ＊ -- 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] Regarding top2psf script
Dear all, I want to reverse transform my CG lipid system to AA. I have been using g_fg2cg but I am getting some errors (like Atoms in the .top are not numbered consecutively from 1). So, I intend to use the script top2psf.plwritten by Dr.Lemkul, so that I can avail the help of VMD in cg2aa conversion. Can we use it for pure lipid systems (say POPC+CHOL+triglyceride+CE)? When I tried to execute it, I am getting the following error Cannot open angles for reading: No such file or directory Thanks for your concern -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] interaction energy
On 4/18/13 2:00 AM, fatemeh ramezani wrote: HI I'm simulating gold-protein interaction by gromacs. after MD simulation I want to calculate interaction energy of each aminoacids with AU surface. Enon-bond = E(vdw) + E(elec) gold atoms charge in simulation were considered 0, then E non-bonded=E(vdw) Is this true? The interaction energy is equal to the van der Waals energy? If charges are zero, then yes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] installing gromacs-4.6.1 with CMake
On 4/18/13 3:09 AM, 中野佑香 wrote: Hi. I'm trying to build a build with cmake-2.8.10.2-linux for 'gromacs-4.6.1' as the build target. First, I extracted gromacs-4.6.1.tar.gz and, create a new folder; build inside the extracted folder. Then, inside build folder, I configured using CMake. $ tar -xvzf gromacs-4.6.1.tar.gz $ cd gromacs-4.6.1 $ mkdir build $ cd build $ cmake .. However, I got an error. -- CMake Error: The source directory /home/okayuka/Gromacs does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. - Inside gromacs-4.6.1 directory, there is certainly CMakeLists.txt. For this, I think cmake mistaking /home/okayuka/Gromacs for /home/okayuka/Gromacs/gromacs-4.6.1 as ' the source directory'. Would you please tell me how correct this mismatch of the source directory? The sequence of commands you have entered above is correct, but that's apparently not what's actually happening in your terminal. The error indicates you are trying to use CMake to build within /home/okayuka/Gromacs, not /home/okayuka/Gromacs/gromacs-4.6.1. That would happen if perhaps you had forgotten to cd into gromacs-4.6.1. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Regarding top2psf script
On 4/18/13 5:15 AM, Venkat Reddy wrote: Dear all, I want to reverse transform my CG lipid system to AA. I have been using g_fg2cg but I am getting some errors (like Atoms in the .top are not numbered consecutively from 1). So, I intend to use the script top2psf.plwritten by Dr.Lemkul, so that I can avail the help of VMD in cg2aa conversion. Can we use it for pure lipid systems (say POPC+CHOL+triglyceride+CE)? When I tried to execute it, I am getting the following error Cannot open angles for reading: No such file or directory My script only works on a single molecule topology. It will not work for a complex system like yours. Perhaps you can process each .itp file separately, which may be of some use, but that will only potentially give you an AA representation of a single molecule. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Applying a Lennard-Jones Gauss potential function for TIP5P water
Greetings, I am simulating a box of TIP5P waters and I would like to know if it is possible to change the standard LJ potential function to a more complex one (LJ-Gauss), while keeping the coulombic interaction standard. The custom potential will act between the oxygen atoms only and has the form: eps*[(sig/r)^12 - 2*(sig/r)^6] - epsG*[exp-(((r-rG)^2) / (2*sigG^2))] where epsG, sigG and rG are new parameters. Can this be accomplished using tables, a custom force field / topology, or other? I would appreciate any suggestions relating to how this can be done. Thanks, Andrish -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Please consider the environment before printing this email. -- 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] Applying a Lennard-Jones Gauss potential function for TIP5P water
On 4/18/13 7:31 AM, Andrish Reddy wrote: Greetings, I am simulating a box of TIP5P waters and I would like to know if it is possible to change the standard LJ potential function to a more complex one (LJ-Gauss), while keeping the coulombic interaction standard. The custom potential will act between the oxygen atoms only and has the form: eps*[(sig/r)^12 - 2*(sig/r)^6] - epsG*[exp-(((r-rG)^2) / (2*sigG^2))] where epsG, sigG and rG are new parameters. Can this be accomplished using tables, a custom force field / topology, or other? I would appreciate any suggestions relating to how this can be done. Tabulated potentials are the best bet. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] installing gromacs-4.6.1 with CMake
Dear Justin, Thank you for your fast reply. cmake was successfully worked after I removed CMakeCache.txt from gromacs-**4.6.1 directory and corrected CMake path in .tcshrc . Thank you! -Yuka 2013/4/18 Justin Lemkul jalem...@vt.edu On 4/18/13 3:09 AM, 中野佑香 wrote: Hi. I'm trying to build a build with cmake-2.8.10.2-linux for 'gromacs-4.6.1' as the build target. First, I extracted gromacs-4.6.1.tar.gz and, create a new folder; build inside the extracted folder. Then, inside build folder, I configured using CMake. $ tar -xvzf gromacs-4.6.1.tar.gz $ cd gromacs-4.6.1 $ mkdir build $ cd build $ cmake .. However, I got an error. --**--** --** CMake Error: The source directory /home/okayuka/Gromacs does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. --**--** --**--- Inside gromacs-4.6.1 directory, there is certainly CMakeLists.txt. For this, I think cmake mistaking /home/okayuka/Gromacs for /home/okayuka/Gromacs/gromacs-**4.6.1 as ' the source directory'. Would you please tell me how correct this mismatch of the source directory? The sequence of commands you have entered above is correct, but that's apparently not what's actually happening in your terminal. The error indicates you are trying to use CMake to build within /home/okayuka/Gromacs, not /home/okayuka/Gromacs/gromacs-**4.6.1. That would happen if perhaps you had forgotten to cd into gromacs-4.6.1. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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 -- ＊ 中野佑香 立教大学 理学研究科化学専攻 博士前期課程 1年 理論創薬・分子設計 常盤研究室 〒171-8501 東京都豊島区西池袋3-34-1 4号館4230教室 Email: yuk...@rikkyo.ac.jp 09cc0...@rikkyo.ac.jp ＊ -- 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: Applying a Lennard-Jones Gauss potential function for TIP5P water
Thanks Justin, I had a look at the manual regarding tabulated potentials... for clarity, The table values must contain: x, f(x), −f(x), g(x), −g(x), h(x), −h(x). For my function then would f(x) = 1/r g(x) = eps*[(sig/r)^12 - 2*(sig/r)^6] and h(x) = -epsG*[exp-(((r-rG)^2) / (2*sigG^2))] ? Also from the manual: The parameters A, B, and C are read from the topology. The type of interaction, Lennard-Jones or Buckingham, is determined by the nbfunc parameter in the [ defaults ] directive of the topology. How would the A,B C terms be applied to my function with 5 constants? What would 'nbfunc' have to be set to? Regards, Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/Applying-a-Lennard-Jones-Gauss-potential-function-for-TIP5P-water-tp5007415p5007418.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Running simulation over openmpi in rsh
Dear Gmx, Is there anyway I can run simulation using mpirun command via rsh? I am using openmpi 1.6 version. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to fix interfacial tension in NPT
Dear Gromacs users, I have runned a semiisotropic NPT simulation for a membrane, I have fixed the pressure in x and y axis and I varied it only in z axis to keep a stable interface. But after simulation the obtained interfacial tension is far bigger than the experimental value. Experimental is 27 mN.m-1 and the simulated one was around 38 mN.m-1. I will be very grateful if you can suggest me which parameters should I check in order to regulate the interfacial tension value. Thank you very much -- 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] Membrane Simulation
Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the “-rotate” and “-center” options on, but when I scale the lipid positions with the perl script (before the energy minimization), the protein moves up, de facto off from the membrane! Obviously I've set very strong position-restraining force on protein, but it moves the same. Probably the problem is trivial, but I can't see it, so any help is much appreciated. Thanks a lot, GIuseppe Cimicata -- View this message in context: http://gromacs.5086.x6.nabble.com/Membrane-Simulation-tp5007421.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] ffnonbonded value of charmm to charmm27 ff
Dear gmx, I m having a confusion of using the literature value of non-bonded ( charmm format) to use in gromacs over charmm27.ff ? For example, the literature reported the Carbon nonbonded as ( sigma =3.83, epsilon -0.0262 ), whereas the charmm27.ff in gromacs- ffnonbonded value listed for Carbon listed as (sigma 0.356359487256, epsilon 0.46024). so whats is the procedure to convert this literature value favor to charmm27 in gromacs? Thanks in advance. Regards Rajiv -- 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] Building Single and Double Precision in 4.6.1?
Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to delete everything from my build directory before running cmake again? One concern is that each time I run cmake, it will download fftw and the regression tests. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, April 15, 2013 11:05 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- 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] Building Single and Double Precision in 4.6.1?
On Thu, Apr 18, 2013 at 6:17 PM, Mike Hanby mha...@uab.edu wrote: Thanks for the reply, so the next question, after I finish building single precision non parallel, is there an efficient way to kick off the double precision build, then the single precision mpi and so on? Or do I need to delete everything from my build directory before running cmake again? Well, most setting can just be changed in the build tree and rerunning cmake build trigger a rebuild, e.g.: $ cmake path/to/source -DGMX_DOUBLE=OFF -DCMAKE_INSTALL_PREFIX=/my/install/path; make install -j; cmake .-DGMX_DOUBLE=ON; make install -j; However, I recommend that you do your builds outside the source tree in separate build directories - or at least in separate directories in the source tree - and just use the same CMAKE_INSTALL_PREFIX for every build. One concern is that each time I run cmake, it will download fftw and the regression tests. If you want to do regression tests of multiple builds, to avoid the downloading, you should download the regressiontests tarball manually and just point cmake to it instead of having it download every time. While you'll need a different FFTW build for double precision, you are right that single precision MPI vs thread-MPI builds would not need a different FFTW. If you want to avoid this (IMHO minor) overhead, compile FFTW manually and just point CMake to it (via CMAKE_PREFIX_PATH). Cheers, -- Szilárd -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Monday, April 15, 2013 11:05 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Building Single and Double Precision in 4.6.1? That's best. GROMACS will take care of a _d suffix for double precision for you. Mark On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote: Howdy, What's the proper procedure for building both single and double precision and installing them to the same directory? For example, is this the proper set of steps? #Build and install single precision cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install cmake .. \ -DGMX_BUILD_OWN_FFTW=ON \ -DGMX_DOUBLE=ON \ -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/4.6.1 \ -DREGRESSIONTEST_DOWNLOAD=ON make make check make install Or is there a more efficient way? Thanks, Mike -- 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 -- 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: Applying a Lennard-Jones Gauss potential function for TIP5P water
On 4/18/13 8:44 AM, Andrish Reddy wrote: Thanks Justin, I had a look at the manual regarding tabulated potentials... for clarity, The table values must contain: x, f(x), −f(x), g(x), −g(x), h(x), −h(x). For my function then would f(x) = 1/r g(x) = eps*[(sig/r)^12 - 2*(sig/r)^6] and h(x) = -epsG*[exp-(((r-rG)^2) / (2*sigG^2))] ? Also from the manual: The parameters A, B, and C are read from the topology. The type of interaction, Lennard-Jones or Buckingham, is determined by the nbfunc parameter in the [ defaults ] directive of the topology. How would the A,B C terms be applied to my function with 5 constants? What would 'nbfunc' have to be set to? Sorry, I have no experience with complex cases like this. Set up a small test case that can be easily verified and try your luck. Tabulated potentials are definitely the way to go though, unless you want to completely overhaul the Gromacs code to implement the new potential equation expression :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] How to fix interfacial tension in NPT
On 4/18/13 10:51 AM, Souilem Safa wrote: Dear Gromacs users, I have runned a semiisotropic NPT simulation for a membrane, I have fixed the pressure in x and y axis and I varied it only in z axis to keep a stable interface. But after simulation the obtained interfacial tension is far bigger than the experimental value. Experimental is 27 mN.m-1 and the simulated one was around 38 mN.m-1. I will be very grateful if you can suggest me which parameters should I check in order to regulate the interfacial tension value. You haven't posted your .mdp file or even stated what force field you're using. Is your force field designed to reproduce such surface tension values? The results are only as good as the model itself, and your usage of it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Membrane Simulation
On 4/18/13 10:59 AM, Giuseppe wrote: Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the “-rotate” and “-center” options on, but when I scale the lipid positions with the perl script (before the energy minimization), the protein moves up, de facto off from the membrane! Obviously I've set very strong position-restraining force on protein, but it moves the same. Probably the problem is trivial, but I can't see it, so any help is much appreciated. You probably haven't set up the protein's location in a box with the same dimensions as the membrane, so it's centered within some different unit cell. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Free energy on GPU?
Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use Verlet cutoff scheme. When I do so with pme electrostatics everything works fine until free energy calculation stage. Something strange happens there: the temperature of the system increases with increase of lambda value with no respect to thermostat (300 at lambda = 0.0 - 500 at lambda = 1.0). Interesting fact that with reaction-field electrostatics everything seemed to work fine but now I cannot be sure that these results are reliable. As I understood from manual there is some issue with Verlet cutoff scheme and free energy calculations. Can I perform TI calculation in GROMACS with GPU acceleration or should I use group cutoffs and forget about GPU? Thanks a lot, Oleg Titov -- 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] Free energy on GPU?
On 4/18/13 2:30 PM, Олег Титов wrote: Dear all. I'm trying to estimate relative solvation enegry of brombenzene (relative to benzene) via thermodynamic integration. Can I perform such calculation in GROMACS with GPU acceleration? As I currently understand to make use of GPU one need to use Verlet cutoff scheme. When I do so with pme electrostatics everything works fine until free energy calculation stage. Something strange happens there: the temperature of the system increases with increase of lambda value with no respect to thermostat (300 at lambda = 0.0 - 500 at lambda = 1.0). Interesting fact that with reaction-field electrostatics everything seemed to work fine but now I cannot be sure that these results are reliable. As I understood from manual there is some issue with Verlet cutoff scheme and free energy calculations. Can I perform TI calculation in GROMACS with GPU acceleration or should I use group cutoffs and forget about GPU? As far as I am aware, free energy calculations are not supported on GPU. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] ffnonbonded value of charmm to charmm27 ff
Identify the equations into which they are inserted. Apply scaling parameters to change the units. Learn to check others' work before investing months of effort ;-) Mark On Thu, Apr 18, 2013 at 5:39 PM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx, I m having a confusion of using the literature value of non-bonded ( charmm format) to use in gromacs over charmm27.ff ? For example, the literature reported the Carbon nonbonded as ( sigma =3.83, epsilon -0.0262 ), whereas the charmm27.ff in gromacs- ffnonbonded value listed for Carbon listed as (sigma 0.356359487256, epsilon 0.46024). so whats is the procedure to convert this literature value favor to charmm27 in gromacs? Thanks in advance. Regards Rajiv -- 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] Autocorrelation of C-N
Chapter 8 is your friend. Find a tool to feed data to g_analyze. Mark On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Users, Could you advise me please how to calculate vector C-N autocorrelation function in my protein along the simulation time? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Running simulation over openmpi in rsh
No idea. Configuring your MPI system is not really on topic for the GROMACS mailing list. I suggest you read your OpenMPI documentation. Mark On Thu, Apr 18, 2013 at 2:58 PM, 라지브간디 ra...@kaist.ac.kr wrote: Dear Gmx, Is there anyway I can run simulation using mpirun command via rsh? I am using openmpi 1.6 version. -- 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] pdb2gmx for small molecules?
Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? Thanks. Warren Gallin-- 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] pdb2gmx for small molecules?
On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? pdb2gmx only knows how to handle what it knows about. There is no generic support for arbitrary compounds. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] pdb2gmx for small molecules?
On 2013-04-18 21:35, Justin Lemkul wrote: On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? pdb2gmx only knows how to handle what it knows about. There is no generic support for arbitrary compounds. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin Try GAFF using the Ambertools and acpype. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Announcement: new version of GridMAT-MD available
Greetings all, I wanted to announce that we have released version 2.0 of GridMAT-MD. Many of you use this program for membrane analysis and I am pleased to note that we have introduced many new features based on your feedback, including trajectory support (multi-frame .pdb and .gro files). Please visit our webpage for details: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ We hope you continue to find our software useful. Please contact me if any issues arise. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] A beginner's question ...
Dear All I am new to GROMACS, I have the following question: What is the difference between Pres. DC and Pressure in g_energy analysis ? Thanks in advance Venkatesh -- 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] A beginner's question ...
On 4/18/13 7:22 PM, Venkatesh Ramakrishnan wrote: Dear All I am new to GROMACS, I have the following question: What is the difference between Pres. DC and Pressure in g_energy analysis ? Pres. DC is the correction applied to the pressure term in dispersion correction when using DispCorr = EnerPres. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Different energy using the identical tpr file
Hello, I have a 2 tpr files which are identical. Then I am doing a single step MD (I put n_step=0) simulation just to compute the total energy of a certain configuration. These tpr files give me different energy values ... when I run it on my computer or on another computer. Even the gromacs version is the same in both computers. I compiled gromacs identical in both computers. Can you help me to figure it out? Thanks Fahimeh -- 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] Announcement: new version of GridMAT-MD available
It seems to be good. However, I always have problem to compile matpack which is needed by xmatrix... I sent the author an email, but never replied.. here is the log file: creating libpng12.la (cd .libs rm -f libpng12.la ln -s ../libpng12.la libpng12.la) make[4]: Leaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' make[3]: Leaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' (cd Matutil ; make ) make[3]: Entering directory `/home/albert/Desktop/matpack/source/Matutil' g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE=X11/xpm.h -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpromannumber.cpp g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE=X11/xpm.h -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpcontextsave.cpp g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE=X11/xpm.h -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpparsetool.cpp g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE=X11/xpm.h -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mpgetopt.cpp mpgetopt.cpp: In member function ‘bool MATPACK::MpGetopt::assign(MATPACK::MpGetopt::OptNode*, const char**, std::string)’: mpgetopt.cpp:314: error: ‘strtol’ was not declared in this scope mpgetopt.cpp:330: error: ‘strtoul’ was not declared in this scope mpgetopt.cpp:345: error: ‘strtod’ was not declared in this scope g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE=X11/xpm.h -c -s -Wall -O3 -fforce-addr -funroll-loops -felide-constructors -I ../../include mptimerqueue.cpp make[3]: *** [mpgetopt.o] Error 1 make[3]: *** Waiting for unfinished jobs make[3]: Leaving directory `/home/albert/Desktop/matpack/source/Matutil' make[2]: *** [static_lib] Error 2 make[2]: Leaving directory `/home/albert/Desktop/matpack/source' make[1]: *** [lib] Error 2 make[1]: Leaving directory `/home/albert/Desktop/matpack' make: *** [allstatic] Error 2 thank you very much Albert On 04/18/2013 11:19 PM, Justin Lemkul wrote: Greetings all, I wanted to announce that we have released version 2.0 of GridMAT-MD. Many of you use this program for membrane analysis and I am pleased to note that we have introduced many new features based on your feedback, including trajectory support (multi-frame .pdb and .gro files). Please visit our webpage for details: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/ We hope you continue to find our software useful. Please contact me if any issues arise. -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
