Re: [gmx-users] installing Gromacs on windows using cygwin

If you use bash just add source /usr/local/gromacs/bin/GMXRC to ~/.bashrc file as separate line, like: echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc or just use your favorite text editor. On Monday, April 23, 2018, 1:57:02 PM GMT+3, Hossein Geraili wrote:

Re: [gmx-users] installing Gromacs on windows using cygwin

Hi, could you please help me with the search!!! source /usr/local/gromacs/bin/GMXRC You may wish to arrange for your login scripts to do this automatically; please search the web for instructions on how to do this for your shell. How can I do that command automatically?? Best ‌ [image:

Re: [gmx-users] installing Gromacs on windows using cygwin

Hi, Follow http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation which instructs you to do the same thing you must have done last time. That has to be done from each shell, or set up to be true for all shells. Mark On Sat, Apr 21,

Re: [gmx-users] installing Gromacs on windows using cygwin

Hi all, I am using Linux, and I followed the installation guide in the Gromacs page exactly, and it seems everything was successful for installation of Gromacs 2018.1. I also at the end typed "gmx pdb2gmx" and it seems that gromacs was installed in all the computer while using that terminal, but

Re: [gmx-users] installing Gromacs on windows using cygwin

Hi, Surely cygwin has its own cmake package, which you should use rather than compile it yourself. Mark On Thu, Apr 19, 2018, 18:02 Hossein Geraili wrote: > Hi all, > I want to install Gromacs on windows 10, and I get the error while > installing Cmake with cygwin. I

[gmx-users] installing Gromacs on windows using cygwin

Hi all, I want to install Gromacs on windows 10, and I get the error while installing Cmake with cygwin. I tried two different version and the error is the same. gmake: *** No rule to make target '/cygdrive/h/Ph.D/Gromacs/ Software/cmake-3.10.3/Source/cmAddCustomCommandCommand.cxx', needed by

[gmx-users] installing Gromacs on windows using cygwin

Hi all, I want to install Gromacs on windows 10, and I get the error while installing Cmake with cygwin. I tried two different version and the error is the same. gmake: *** No rule to make target '/cygdrive/h/Ph.D/Gromacs/Software/cmake-3.10.3/Source/cmAddCustomCommandCommand.cxx', needed by

Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

Thanks for your input. Will install it on WLS and run some simulations. The GPU acceleration not working might be a current limitation within WLS. Will look into it. Abbas From: P C Kroon Sent: Monday, 11 December, 12:37 Subject: Re: [gmx-users] Installing gromacs on the windows 10 linux

Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

s.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem Yes! I have gromacs installed and running on my machine. Dan On Sat, Dec 9, 2017 at 4:02 AM A. Alamir <alami...@hotmail.com> wrote: > Dear all, > > I would like to know i

Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

Thanks for your feedback. Abbas From: Dan Gil<mailto:dan.gil9...@gmail.com> Sent: Saturday, December 9, 2017 5:43 PM To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> Cc: gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se> Subje

Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

Yes! I have gromacs installed and running on my machine. Dan On Sat, Dec 9, 2017 at 4:02 AM A. Alamir wrote: > Dear all, > > I would like to know if using gromacs on the Windows 10 ubuntu Linux > subsystem (WLS) is supported. On WLS the gromacs package can be directly >

[gmx-users] Installing gromacs on the windows 10 linux subsystem

Dear all, I would like to know if using gromacs on the Windows 10 ubuntu Linux subsystem (WLS) is supported. On WLS the gromacs package can be directly installed via the Ubuntu apt-get command. I know there are other windows-based alternatives to installing/using gromacs (ex. Cygwin), but on

Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

Hi, So did you try the other half of my suggestion? (And ask harder - installing gcc is no harder than installing icc, and there is no point buying CUDA GPUs without funding for people to install compilers that support them.) Mark ‪On Thu, May 26, 2016 at 11:39 AM ‫יוכבד‬‎

Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

The problem is the gcc installed on our cluster is to old and it is not possible to upgrade at the moment. On Wed, May 25, 2016 at 1:44 PM, Mark Abraham wrote: > Hi, > > You need to follow Intel's instructions for accessing the compiler - > including running their

Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

Hi, You need to follow Intel's instructions for accessing the compiler - including running their magic scripts from each shell that you want to compile from. (Or save yourself some pain, use gcc, and probably run slightly faster.) Mark ‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎

[gmx-users] Installing GROMACS 5.1.2 om GPU

Hi I've been having lots of trouble installing gromacs on our GPU machine. I have Intel2015 Compilers on my machine which are identified correctly during configuration. /private/gnss/cmake-2.8.11.2/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2 -DGMX_GPU=on

Re: [gmx-users] installing gromacs-5.0.5

i think you should install by downloading source file and CUDA toolkit for your GPU.may i know what is your GPU? i also wondering about GPU and CUDA ? Nikhil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] installing gromacs-5.0.5

Hello everybody; I want to install gromacs-5.0.5 in ubuntu-14.04 using the installation instruction in the website "gromacs.org", but in the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" line I got this error: -- No compatible CUDA toolkit found (v4.0+), disabling native GPU

[gmx-users] installing GROMACS

Hi; I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the gromacs.org, but I got an error after typing "cmake .. " line, then I tried "sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I want the gromacs-5.0.5. what should I do? Thank you,

Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ??

, November 19, 2014 4:43 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ?? On Thu, Nov 20, 2014 at 12:08 AM, Soren Wacker swac...@ucalgary.ca wrote: Hi, another question: Is it possible to install

Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ??

...@gmail.com] Sent: Friday, November 21, 2014 2:22 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ?? On Fri, Nov 21, 2014 at 2:32 AM, Soren Wacker swac...@ucalgary.ca wrote: I tried both, with the same result. I can

Re: [gmx-users] Installing gromacs 5.0.2 single precision with CUDA and MPI ??

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, November 19, 2014 6:08 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Installing gromacs 5.0.2 single

Re: [gmx-users] Installing gromacs 5.0.2 double precision with shared fftw libraries

On Wed, Nov 19, 2014 at 7:25 PM, Soren Wacker swac...@ucalgary.ca wrote: Hi, I have trouble to install gromacs 5.0.2 in double precision with shared fftw libraries. During the cmake process I get: Could not find fftw3 library named libfftw3, please specify its location in CMAKE_PREFIX_PATH

Re: [gmx-users] Installing gromacs 5.0.2 double precision with shared fftw libraries

, November 19, 2014 3:01 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Installing gromacs 5.0.2 double precision with shared fftw libraries On Wed, Nov 19, 2014 at 7:25 PM, Soren Wacker swac...@ucalgary.ca wrote: Hi, I have trouble to install gromacs 5.0.2 in double

Re: [gmx-users] Installing gromacs 5.0.2 double precision with shared fftw libraries

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Carsten Kutzner [ckut...@gwdg.de] Sent: Wednesday, November 19, 2014 11:43 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Installing

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

09:19:14 +0800 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster What he meant was to specify full path of your cmake, i.e. /work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY. (and so on); instead of just typing cmake .. -DGMX_FFT_LIBRARY This is really

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

2014 22:46:29 +0900 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster I am thinking of using gcc and g++ now. Kindly provide further suggestions. http://hpc.ucla.edu/hoffman2/software/compilers http://lmgtfy.com/?q=difference+between+gcc+and+g%2B%2B http://lmgtfy.com/?q=gcc

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

: Szilárd Páll pall.szil...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Cc: Discussion list for GROMACS users gromacs.org_gmx-users@maillist.sys.kth.se Date: Sun, 9 Nov 2014 23:16:23 +0100 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster On Sun, Nov 9

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

@maillist.sys.kth.se Date: Sun, 9 Nov 2014 23:16:23 +0100 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster On Sun, Nov 9, 2014 at 9:17 PM, Szilárd Páll pall.szil...@gmail.com wrote: That looks like it could actually be a compiler/linker or cmake crash. Could you run: $ make

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

...@gromacs.org Cc: Date: Fri, 07 Nov 2014 16:26:56 -0500 Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster On 11/7/14 4:20 PM, Agnivo Gosai wrote: Dear Users I checked and found that the CMAKE version installed in my university cluster is 2.6-patch 4 however GROMACS 4.6.7 requires

Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

ubject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel ClusterOn 11/7/14 4:20 PM, Agnivo Gosai wrote: Dear Users I checked and found that the CMAKE version installed in my university cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher. So I installed CMAKE 2.8.11 in my local work

[gmx-users] Installing gromacs 4.6.6 with gsl 1.16

Dear Gromacs users, am trying to install gromacs 4.6.6 with GSL. I have installed fftw3 and GSL in separate directories on Desktop and linked them to Gromacs in the follwing command. /home/user1/Desktop/cmake-2.8.12.2-Linux-i386/bin/ccmake ../ -DGMX_MPI=ON -DGMX_SIMD=SSE2 -DGMX_DOUBLE=ON

Re: [gmx-users] Installing gromacs 4.6.6 with gsl 1.16

On 9/1/14, 3:26 AM, B P wrote: Dear Gromacs users, am trying to install gromacs 4.6.6 with GSL. I have installed fftw3 and GSL in separate directories on Desktop and linked them to Gromacs in the follwing command. /home/user1/Desktop/cmake-2.8.12.2-Linux-i386/bin/ccmake ../ -DGMX_MPI=ON

Re: [gmx-users] Installing gromacs 4.6.6 with gsl 1.16

On Mon, Sep 1, 2014 at 4:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/1/14, 3:26 AM, B P wrote: Dear Gromacs users, am trying to install gromacs 4.6.6 with GSL. I have installed fftw3 and GSL in separate directories on Desktop and linked them to Gromacs in the follwing command.

Re: [gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

Ok. Now I think it works... almost! Now I want to check gromacs for correctness. I downloaded the tarball, unpacked it and opened the new folder with the console. Then I inserted source /usr/local/gromacs/bin/GMXRC (it is really there, I looked for it!) and with ./gmxtest.pl all I started the

Re: [gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

Thanks for you reply Szilárd Páll-2! Meanwhile I have installed gromacs and it does not work for me. Checking gromacs with the degression test resolved that almost everything is going wrong! I am sorry to ask you but is there a way to install gromacs and/or FFTW3 to a default path? I will retry

Re: [gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

On 1/19/14, 6:48 PM, GtrAngus wrote: So what I did until now: I unpacked the *.tar file to the folder: I made a new directory with just like in the quick and dirty installation for gromacs. When I am running cmake checks and looks for some stuff (I am sorry to tell this way because

[gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

Hi guys, I am trying to install Gromacs 4.6.5 on Kubuntu. My Kubuntu skills are not that good, so I kept close to the Install Instructions. I skipted the Quick and Dirty Instrucitons and now I should be at the point 4.1 Configuring with CMake. When I insert cmake .., I recieve: Can anyone tell

Re: [gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

Hi Mark, the reason why I am confused is, that I thought cmake checks if everything is fine or not. So at the point I tried cmake .. for the first time, cmake started all these tests and finally I got the answer I should install FFTW3 and so I did. I did this with typing make. Because make

Re: [gmx-users] Installing Gromacs 4.6.3 using Cygwin

On 13.12.2013 18:01, chem grad wrote: Thank you so much! Gromacs seems to be installed properly now. but mdrun doesn't work, right? M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Installing Gromacs 4.6.3 using Cygwin

On 13.12.2013 21:38, chem grad wrote: I cannot convince cygwin to source the gromacs files properly (well, at least I think that's the problem). When I enter luck into the command line it returns the luck: command not found error message. Also, both commands I have entered (pdb2gmx and mdrun)