[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 exper

[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

[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 analys

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 appr

RE: [gmx-users] transport properties

macs.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) f

[gmx-users] NAMD simulation in Gromacs

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 ?   Secondly can I convert NAMD output files into g

Re: [gmx-users] NAMD simulation in Gromacs

rk Abraham wrote: - Original Message ----- From: oguz gurbulak 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 > simu

[gmx-users] Re: NAMD simulation in Gromacs

wrote: From: Roland Schulz Subject: Re: NAMD simulation in Gromacs To: "oguz gurbulak" , "Discussion list for GROMACS users" Date: Thursday, September 30, 2010, 6:28 PM Oguz, On Thu, Sep 30, 2010 at 4:52 PM, oguz gurbulak wrote: Dear Dr. Roland Schulz,   Tha

[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

[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 h

Re: [gmx-users] non-equilibrium MD simulations

ers" 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 yo

[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 too

[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

Re: [gmx-users] install Gromacs 4.0.4 on Linux Fedora 8

Linux Fedora 8 To: "Discussion list for GROMACS users" 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 g

[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 mistak

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 wrote: From: Vitaly V. Chaban Subject: [gmx-use

[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 progr

[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 u

[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-dod

[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 g

Re: [gmx-users] pdb files

tin A. Lemkul Subject: Re: [gmx-users] pdb files To: gurbulako...@yahoo.com, "Discussion list for GROMACS users" 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

Re: [gmx-users] pdb files

: From: Justin A. Lemkul Subject: Re: [gmx-users] pdb files To: "Discussion list for GROMACS users" 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 editi

[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 p

[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 lis

[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 ?

[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@grom