[gmx-users] trajectory analysis
Dear All, I want to ask some questions about trajectory analysis. I have some md simulation output files that includes coordinate, force and velocity information. And these files are huge ( more than 5 GB ) . Could you please recommend a free text editor which works on Linux or Windows to open and editthese huge files? And I will run these files with fortran codes and get again huge output files . In order to do this operation faster and seamlessly what should I do ? Which facilities do I have on pc ? Could you please share your experiences with me ? Thanks for any help. Kind regards.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make_ndx and rdf
Dear Justin, Of course I tried typing help at the make_ndx prompt but I couldn't generate a .ndx file for my purposes. I strongly need expert help for using make_ndx tool. I'm trying to generate .ndx file for more than one week. Finally I decided to ask it to mailing list. So I will be appreciate for any help. Thanks for your help. From: Justin A. Lemkul jalem...@vt.edu To: Molecular Dynamics moleculardynam...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, October 3, 2011 5:17 PM Subject: Re: [gmx-users] make_ndx and rdf Molecular Dynamics wrote: Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the make_ndx examples in gromacs wiki page but couldn't reach the wiki page. Could you please help me about generating .ndx file ? Carbon in group 1 hydrogen in group 2 oxygen in group 2 group 2 is water I will be gratefull for your helps. Have you tried typing help at the make_ndx prompt? You'll get tons of information, including the commands needed to create the groups you want. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] gromacs tools and namd
Dear All, I'm trying to use some gmx 4.5 tools like g_rdf, g_order, g_msd, g_hbond. To do it I composed a top file using psf and dcd files with topotools1.2 in vmd and generated a tpr file but also I saw some notes below on terminal. Do any of these notes will cause a problem when making analysis ? Should I consider them ? For example I want to calculate rdf for atom-atom or atom-molecules not for groups. What should I do generally to make analysis for atoms and molecules ? ** Select a reference group and 1 group Group 0 ( System) has 3760 elements Group 1 ( Other) has 3760 elements Group 2 ( A) has 380 elements Group 3 ( B) has 3000 elements Group 4 ( C) has 380 elements ** However, do I need to generate a .ndx file for each gmx analysis tools ? make_ndx -f .tpr -o .ndx ( for example ) Thank you very much for your attention. Best regards * Generated 105 of the 105 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 105 of the 105 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'molecule0' Excluding 3 bonded neighbours molecule type 'molecule1' Excluding 3 bonded neighbours molecule type 'molecule2' NOTE 1 [file gromacs.top, line 292]: System has non-zero total charge: -4.00e-03 NOTE 2 [file gromacs.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file gromacs.top]: The largest charge group contains 14 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 1040 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 11277.00 Largest charge group radii for Coulomb: 0.535, 0.535 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 21x21x168, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.34 This run will generate roughly 89 Mb of data There were 3 notes Are these notes * -- 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] initial structures for md simulations
Dear All, I want to generate some initial crystalline structures of my target molecules for md simulations. Are there any free softwares to do this? And are there any complete sources that give the theoretical structures of organic molecules ( like hydrocarbons ) determined by the experiments and give the x-ray, neutron scattering, NMR, IR or Raman results of organic molecules apart from the articles ? Could you please share your thoughts about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: NAMD simulation in Gromacs
Dear Dr. Roland Schulz, Thank you very much for your attention. I have Amber type ff that includes bond, angle, dihedral and nonbounded interaction terms in Charmm file format. Should I use the patch to generate a gromacs topology from psf file ? I have NAMD created.coor and .vel files that have the final coordinates and velocities. Also I have a dcd trajectory file. And according to these informations what is the next step after getting the gromacs topology file to continue a NAMD simulation in Gromacs ? What should I do ? Kind regards. --- On Thu, 9/30/10, Roland Schulz rol...@utk.edu wrote: From: Roland Schulz rol...@utk.edu Subject: Re: NAMD simulation in Gromacs To: oguz gurbulak gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, September 30, 2010, 6:28 PM Oguz, On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak gurbulako...@yahoo.com wrote: Dear Dr. Roland Schulz, Thank you very much for your attention. I would like to have a copy of patch that generates gromacs topology from psf file. And could you please explain how to use this patch in detail ? Because I have no information on Pär's scripts. Do you have standard CHARMM or Amber FF? Than you don't need to convert the FF because it is already part of GROMACS. I think, In order to continue a NAMD simulation in Gromacs I should first save the last coordinates (.coor file in namd ) as a pdb file and convert it into gro file . But there are many ways to get a gro file no you don't need to convert the coordinate file or get the last frame. - using pdb2gmx ( but I should choose the force field in gromacs. This may be a problem. ) By the way, I changed CHARMM force field and use Amber type force field in NAMD. Don't understand what you mean? Do you use CHARMM or Amber FF? If it is a standard molecule (e.g. protein), it will be much easier to just use pdb2gmx to generate the topology. Could you share your ideas about this process ? What should I do ? You would just do everything the same way as setting up a new simulation and use the last frame as starting structure. Make sure you use a structure which includes both coordinates and velocities. Is there a way to get a tpr file from NAMD files? No. Not automatically. You need to get all the input files (grompp.mdp, topol.top, conf.gro) and then run grompp to generate your tpr. Roland Kind regards. Oguz GURBULAK Ph.D. Student Ege University - Faculty of Science Department of Physics Branch of Atomic and Molecular Physics -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NAMD simulation in Gromacs
Dear All, I think, In order to continue a NAMD simulation in Gromacs I should first save the last coordinates (.coor file in namd ) as a pdb file and convert it into gro file . But there are many ways to get a gro file - using pdb2gmx ( but I should choose the force field in gromacs. This may be a problem. ) By the way, I changed CHARMM force field and use Amber type force field in NAMD. -using VMD ( but I’m not sure if it works ) -using editconf in gromacs ( if you have the structure in pdb format, you can convert it into a .gro file with editconf. Also, the size of the box should be specified (in gromacs the length for the vectors a, b and c is in nm, not angstrom) editconf -f file.pdb -o file.gro -box a b c -angles 90 90 90 Could you share your ideas about this process ? What should I do ? Then I should convert the psf file into gromacs top file. If I get a gro and top file correctly, I can continue NAMD simulation in Gromacs. Is it true ? I examined the gromacs tutorials. And I think I must have a tpr and a xtc file to use gromacs analysis tools. I can get a xtc file from NAMD dcd file but how can I create a tpr file ? Is there a way to get a tpr file from NAMD files? Kind regards. --- On Thu, 9/30/10, Roland Schulz rol...@utk.edu wrote: From: Roland Schulz rol...@utk.edu Subject: Re: [gmx-users] NAMD simulation in Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, September 30, 2010, 10:13 AM On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: oguz gurbulak gurbulako...@yahoo.com Date: Thursday, September 30, 2010 21:38 Subject: [gmx-users] NAMD simulation in Gromacs To: gmx-users@gromacs.org Dear All, I performed a 50 ns md simulation using NAMD and want to continue this simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation in Gromacs ? If so, could you please give me the information about this process ? Not really. You would need to generate a .top in the normal way, and this process cannot use any topology information that NAMD was using. You could start the GROMACS simulation from the endpoint of the NAMD simulation, but it would not be continuous in any sense. We have a patch to psfgen to generate gromacs topology. We plan to put this on our website. While it hasn't be uploaded yet, please write me in case you would like to have a copy. It does convert the parameter files. We use Pär's scripts to do that part. Secondly can I convert NAMD output files into gromacs output files and use gromacs analysis tools ? Could you please also give me the information about this issue ? If you have VMD installed then GROMACS is supposed to be able to link to its libraries to enable GROMACS tools to read any file format that VMD can read, which will include all NAMD formats. I'm unaware that anybody has written any documentation about this, however. That's probably the path of least resistance. Yes as long as VMD is installed (and GROMACS is compiled with DLOPEN support - which is default) all the GROMACS tools automatically can read most VMD supported format. The exception is any format which doesn't record the number of atoms (as e.g. Amber). Roland -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] multiple time step
Dear All, Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a query about analysis
Dear All, I study on molecular dynamics simulations of organic molecules. I want to learn that Is there an excel-like program that accepts more data set ( for instance output info for 5000 records ) in order to make analysis ? Could you please give me some suggestions about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] non-equilibrium MD simulations
Hi Justin, I study on md simulations of hydrocarbons and I want to apply an electrical field in one direction in my md simulations. Is it possible to do this in Gromacs ? and generally what can be done to simulation system about non-equilibrium MD in Gromacs ? I didn't find any information about this issue. So I will be very happy if you provide me some information about non-equilibrium MD ? Best regards --- On Mon, 2/1/10, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] non-equilibrium MD simulations To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, February 1, 2010, 7:08 AM oguz gurbulak wrote: Dear All, I'm searching for a non-equilibrium MD tutorial done with Gromacs. Could you please help me to find a NEMD tutorial ? Non-equilibrium can encompass a variety of topics, so if you want specific advice, you'll have to be more specific. And, as I just mentioned to someone else: http://lists.gromacs.org/pipermail/gmx-users/2010-February/048498.html -Justin Thank in advance . -- 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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] non-equilibrium MD simulations
Dear All, I'm searching for a non-equilibrium MD tutorial done with Gromacs. Could you please help me to find a NEMD tutorial ? Thank in advance . -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] workshop for Gromacs
Dear Gromacs Developers, I'm intested in a workshop for Gromacs. Is there a workshop planned in 2010 ? Kind Regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] transport properties
Dear K. Chae, Thank you very much for your answer. I computed velocity auto-correlation (VAC) functions , but how can I integrate velocity auto-correlation (VAC) functions to get Diffusion coefficient using xmgrace software ? I have just used xmgrace to plot md result for analysis. And I have a limited information using xmgrace. Could you please explain the integration procedure in xmgrace ? I will be very grateful if you can help me to learn how to calculate Diffusion coefficient . Thanks in advance for your helps. Best regards, --- On Tue, 4/28/09, kyungchan chae ckcu...@umich.edu wrote: From: kyungchan chae ckcu...@umich.edu Subject: RE: [gmx-users] transport properties To: 'Discussion list for GROMACS users' gmx-users@gromacs.org Date: Tuesday, April 28, 2009, 9:52 AM Once you have correlation results then xmgrace software can do the integration. Regards From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of oguz gurbulak Sent: Tuesday, April 28, 2009 10:25 AM To: gmx-users@gromacs.org Subject: [gmx-users] transport properties Dear All, I'm trying to calculate self diffusion coefficient from velocity auto-correlation (VAC) functions using Green-Kubo relation in figure I attached to the mail. I couldn’t solve how to integrate the velocity auto-correlation (VAC) functions to get Diffusion coefficient. Could you please give me some information about this issue ? Could you suggest some software to integrate the VAC function ? Thanks in advance for your helps. Best regards, -Inline Attachment Follows- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] using Gaussian with Gromacs
Dear All, I want to use the partial charges that were generated with Gaussian 3 for my molecules. How can I adopt the charges into the Gromacs ? Could you give me some information about this procedure ? Sincerely, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] get a top file to run md simulation
Dear Users, I'm trying to obtain .gro and top files successfuly for my n-alkanes molecules and want to run md simulations both using oplsaa and Gromos96 force fields seperately. Then I will compare the results of two md runs. I think that I can generate itp files for Gromos96 force fields using prodgr server and use them for md. But I sholud write itp files for each molecules I want to use for oplsaa . Lets say that I produced itp files, How can I use for example two different itp files and generate a top file like in below. I'm confused about this. Could you give me the information about this procedure ? Sincerely #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb files
Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On Sat, 3/7/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb files
Will I write two .rtp files for two different molecules ? or Will I write one rtp file that includes all parameters of these two molecules ? And how can I use the rtp file when creating the input files ( .gro and .top ) ? Thanks in advance --- On Thu, 3/12/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, March 12, 2009, 12:11 PM oguz gurbulak wrote: Dear Justin, Can I get a itp file tempate for OPLS-AA according to your suggestions below and editing the itp file for my molecule. Is it possible to do this ? Or is there an alternative way apart from manually writing the itp file for OPLS-AA ? You're stuck either writing an .rtp entry for use with pdb2gmx, or writing the .itp yourself. -Justin Thanks in advance You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). --- On *Sat, 3/7/09, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, March 7, 2009, 9:28 AM oguz gurbulak wrote: Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? You will not want to create a topology from these files, because pdb2gmx would create a huge mess of files to deal with (a different topology for each chain). What you want is to do is to create .itp files for each individual molecule type in your system. This will probably have to be done by hand if you want to use OPLS-AA. Depending on the complexity of your molecule, you may be able to use an .rtp entry, but I would suggest processing a single molecule of this type with pdb2gmx to create a .top for that molecule (which can be converted to a .itp for later use). Do not use the Gromacs force field (ffgmx); it is deprecated and should not be used for new simulations. Use a newer Gromos96 variant. You can get Gromos96-compatible topologies from the PRODRG 2.5 server, but be warned that the charges and charge groups assigned by PRODRG are often inconsistent and unsatisfactory, requiring manual alteration and validation. Summary: 1. Create .itp files for each molecule type individually. 2. Construct a .top yourself, which would be as simple as: #include ffoplsaa.itp #include molecule_A.itp #include molecule_B.itp #include spc.itp #include ions.itp [ system ] packmol system [ molecules ] Molecule_A N Molecule_B N SOL N (then whatever ions you need, if any) -Justin Sincerely ___ gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[gmx-users] pdb files
Dear All, I want to use packmol pdb files that includes one or two different types of molecules. And I seached Gromacs manuals, tutorials and mail archives in order to have enough information about using packmol pdb files in Gromacs. But I couldn't find any information. So Could you please give me the information about this ? How can I use a packmol pdb file for oplsaa and gromacs united-atom force field in generating .gro and .top files for md simulations? Sincerely ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] using pdb2gmx
Dear All, I'm trying to create gro and .top files using pdb2gmx. I created n-dodecane.pdb using Chem3D and got 100 molecules using packmol. I added TER cards between each seperate molecules. Then I tried to get gro and .top files using the commands in below : pdb2gmx –ff G43a2 –f n-dodecane.pdb –o n-dodecane.gro –p n-dodecane.top pdb2gmx –ff G43a2 –f n-dodecane.packmol100.pdb –o n-dodecane.gro –p n-dodecane.top ( added TER cards ) pdb2gmx –ff G43a2 –f n-dodecane.packmol100.pdb –o n-dodecane.gro –p n-dodecane.top I couldn't get gro and .top files. Could you please help me to get gro and .top files successfuly ? I also need some information about using packmol pdb file in Gromacs. I want to run md for 100 n-dodecane molecules. Thank you very much for your attention. Sincerely ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about force fields
Dear All, I'm planing to do md simulations for n-alkane molecules. I use Gromacs 4.0.4. I tried to use oplsaa, but I couldn't create .gro and top files. I created my pdb file using Chem3d. I want to ask if I can use oplsaa for n-alkanes. And could you suggest me some force fields that can be used for n-alkanes molecules ? Sincerely, ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a question about analysis
Dear All, I converted the mdcrd ( coordinates, box sizes ) and mdvel ( velocities ) Amber trajectory files for every md record into the pdb format using ptraj in Amber. Can I use these pdb files in Gromacs for performing analysis ? Or Will I need to have some extra files to use analysis programs of Gromacs ? I will only use g_msd , g_velacc , g_energy for calculating viscosity. I'm waiting for your advices. Sincerely ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] install Gromacs 4.0.4 on Linux Fedora 8
Dear All, I'm trying to install Gromacs 4.0.4 on Linux Fedora 8 . But I got this error in therminal: [r...@fencevrepc-84-23 gromacs-4.0.4]# ./configure --prefix=/usr/local/gromacs-4.0.4 --disable-float --program-suffix= checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. What should I do to pass this error ? Could you please help me to install Gromacs successfully to my pc ? And Is there a complete source about installing Gromacs to Linux Fedora ? Thank you very much for your attention. Sincerely ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] install Gromacs 4.0.4 on Linux Fedora 8
Dear Justin, I'm new to Gromacs. I attached the config.log file to the mail. Could you please explain what the neccessary files or operations I should do ? Sincerely --- On Fri, 2/27/09, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] install Gromacs 4.0.4 on Linux Fedora 8 To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, February 27, 2009, 9:07 AM oguz gurbulak wrote: Dear All, I'm trying to install Gromacs 4.0.4 on Linux Fedora 8 . But I got this error in therminal: [r...@fencevrepc-84-23 gromacs-4.0.4]# ./configure --prefix=/usr/local/gromacs-4.0.4 --disable-float --program-suffix= checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. So what do you find in config.log? You are probably missing some other prerequisites (libraries, headers, etc). -Justin What should I do to pass this error ? Could you please help me to install Gromacs successfully to my pc ? And Is there a complete source about installing Gromacs to Linux Fedora ? Thank you very much for your attention. Sincerely ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by gromacs configure 4.0.4, which was generated by GNU Autoconf 2.61. Invocation command line was $ ./configure --prefix=/usr/local/gromacs-4.0.4 --disable-float --program-suffix= ## - ## ## Platform. ## ## - ## hostname = fencevrepc-84-23.ege.edu.tr uname -m = i686 uname -r = 2.6.26.8-57.fc8 uname -s = Linux uname -v = #1 SMP Thu Dec 18 19:19:45 EST 2008 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = i686 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/kerberos/sbin PATH: /usr/kerberos/bin PATH: /usr/lib/ccache PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /sbin PATH: /bin PATH: /usr/sbin PATH: /usr/bin PATH: /usr/X11R6/bin PATH: /usr/local/amber9/exe PATH: /usr/local/c32b2/exec/gnu PATH: /root/bin PATH: /usr/local/amber9/exe PATH: /usr/local/c32b2/exec/gnu ## --- ## ## Core tests. ## ## --- ## configure:2087: checking build system type configure:2105: result: i686-pc-linux-gnu configure:2127: checking host system type configure:2142: result: i686-pc-linux-gnu configure:2180: checking for a BSD-compatible install configure:2236: result: /usr/bin/install -c configure:2247: checking whether build environment is sane configure:2290: result: yes configure:2318: checking for a thread-safe mkdir -p configure:2357: result: /bin/mkdir -p configure:2370: checking for gawk configure:2386: found /bin/gawk configure:2397: result: gawk configure:2408: checking whether make sets $(MAKE) configure:2429: result: yes configure:2612: checking how to create a ustar tar archive configure:2625: tar --version tar (GNU tar) 1.17 Copyright (C) 2007 Free Software Foundation, Inc. License GPLv2+: GNU GPL version 2 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written
[gmx-users] Re: install Gromacs 4.0.4 on Linux Fedora 8
Dear Justin,
I'm new to Gromacs. I attached the config.log file
to the mail. Could you please explain what the neccessary files or
operations I should do ?
Sincerely
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by gromacs configure 4.0.4, which was
generated by GNU Autoconf 2.61. Invocation command line was
$ ./configure --prefix=/usr/local/gromacs-4.0.4 --disable-float --program-suffix=
## - ##
## Platform. ##
## - ##
hostname = fencevrepc-84-23.ege.edu.tr
uname -m = i686
uname -r = 2.6.26.8-57.fc8
uname -s = Linux
uname -v = #1 SMP Thu Dec 18 19:19:45 EST 2008
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = i686
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/kerberos/sbin
PATH: /usr/kerberos/bin
PATH: /usr/lib/ccache
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /sbin
PATH: /bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /usr/X11R6/bin
PATH: /usr/local/amber9/exe
PATH: /usr/local/c32b2/exec/gnu
PATH: /root/bin
PATH: /usr/local/amber9/exe
PATH: /usr/local/c32b2/exec/gnu
## --- ##
## Core tests. ##
## --- ##
configure:2087: checking build system type
configure:2105: result: i686-pc-linux-gnu
configure:2127: checking host system type
configure:2142: result: i686-pc-linux-gnu
configure:2180: checking for a BSD-compatible install
configure:2236: result: /usr/bin/install -c
configure:2247: checking whether build environment is sane
configure:2290: result: yes
configure:2318: checking for a thread-safe mkdir -p
configure:2357: result: /bin/mkdir -p
configure:2370: checking for gawk
configure:2386: found /bin/gawk
configure:2397: result: gawk
configure:2408: checking whether make sets $(MAKE)
configure:2429: result: yes
configure:2612: checking how to create a ustar tar archive
configure:2625: tar --version
tar (GNU tar) 1.17
Copyright (C) 2007 Free Software Foundation, Inc.
License GPLv2+: GNU GPL version 2 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by John Gilmore and Jay Fenlason.
configure:2628: $? = 0
configure:2668: tardir=conftest.dir eval tar --format=ustar -chf - $tardir conftest.tar
configure:2671: $? = 0
configure:2675: tar -xf - conftest.tar
configure:2678: $? = 0
configure:2691: result: gnutar
configure:3297: checking for cc
configure:3313: found /usr/lib/ccache/cc
configure:3324: result: cc
configure:3360: checking for C compiler version
configure:3367: cc --version 5
cc (GCC) 4.1.2 20070925 (Red Hat 4.1.2-33)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3370: $? = 0
configure:3377: cc -v 5
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --with-cpu=generic --host=i386-redhat-linux
Thread model: posix
gcc version 4.1.2 20070925 (Red Hat 4.1.2-33)
configure:3380: $? = 0
configure:3387: cc -V 5
cc: '-V' option must have argument
configure:3390: $? = 1
configure:3413: checking for C compiler default output file name
configure:3440: ccconftest.c 5
/usr/local/bin/ld: unrecognized option '--build-id'
/usr/local/bin/ld: use the --help option for usage information
collect2: ld returned 1 exit status
configure:3443: $? = 1
configure:3481: result:
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME gromacs
| #define PACKAGE_TARNAME gromacs
| #define PACKAGE_VERSION 4.0.4
| #define PACKAGE_STRING gromacs 4.0.4
| #define PACKAGE_BUGREPORT gmx-users@gromacs.org
| #define PACKAGE gromacs
| #define VERSION 4.0.4
| #define GMX_DOUBLE
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME Fri Feb 27 17:09:01 EET 2009
| #define BUILD_USER r...@fencevrepc-84-23.ege.edu.tr
| #define BUILD_MACHINE Linux 2.6.26.8-57.fc8 i686
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:3488: error: C compiler cannot create executables
See `config.log' for more details.
## ##
## Cache variables. ##
## ##
ac_cv_build=i686-pc-linux-gnu
ac_cv_env_CCASFLAGS_set=
ac_cv_env_CCASFLAGS_value=
Re: [gmx-users] Re: install Gromacs 4.0.4 on Linux Fedora 8
Dear Vitaly, Firstly, Thank you very much for your attention. Could you help me to find the build-essential package for Gromacs ? Sincerely --- On Fri, 2/27/09, Vitaly V. Chaban vvcha...@gmail.com wrote: From: Vitaly V. Chaban vvcha...@gmail.com Subject: [gmx-users] Re: install Gromacs 4.0.4 on Linux Fedora 8 To: gmx-users@gromacs.org Date: Friday, February 27, 2009, 9:29 AM Install build-essential package on your system. -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, mob.: +38-097-8259698 ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] analysis using Gromacs tools
Dear All, I'm planning to use Gromacs for analysis with Amber trajectory files ( mdcrd, rst files ). And I found a script that converts Amber mdcrd files to Gromacs-compatible .xtc files. I want to learn that if Gromacs-compatible .xtc files are enough to perform an analysis using Gromacs tools ? or Will I have to have some other files for analysis in Gromacs ? I’m waiting for your suggestions and helps. Thank you very much for your attention. Sincerely ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
