[gmx-users] Gromacs in UBUNTU

Mon May 18 14:10:31 CEST 2015

Hi,

Did you go and read the webpage that is suggested by the rest of that
message?

Mark

On Mon, May 18, 2015 at 12:57 PM Sanchaita Rajkhowa <srajkhowa18 at gmail.com>
wrote:

> sorry..
>
> I mean pdb2gmx, editconf, genion, grompp and mdrun.... even it has genbox
> but it says
>
> "This tool has been removed from Gromacs 5.0. "
>
> On 18 May 2015 at 15:38, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > Hi,
> >
> > What "other commands" are working? Please be specific, we don't have time
> > to spend on guesses :-)
> >
> > Mark
> >
> > On Mon, 18 May 2015 11:06 Sanchaita Rajkhowa <srajkhowa18 at gmail.com>
> > wrote:
> >
> > > Hi
> > >
> > > actually all other commands are working fine. only when I am runing:
> > >
> > > ----------------------------------
> > > g at chandan:~$ gmx solvate -cp protein.pdb -cs tip4p.gro -p topol.top -o
> > > solv.pdb
> > > No command 'gmx' found, did you mean:
> > >  Command 'gm' from package 'graphicsmagick' (universe)
> > >  Command 'gcx' from package 'gcx' (universe)
> > >  Command 'gmt' from package 'libgenome-perl' (universe)
> > >  Command 'ngmx' from package 'gromacs' (universe)
> > > gmx: command not found
> > > -----------------------------------
> > >
> > > this error is coming.
> > >
> > > ------------------------
> > > "gmx solvant doesn't exist, of course, but I assume that was a typo!"
> > >
> > > I have all options but its not working and even it doesn't show like
> > other
> > > commands in the installation dir /soft/gmx504/bin/....
> > >
> > > what else to try!!
> > >
> > >
> > >
> > > On 18 May 2015 at 13:11, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> > >
> > > > Hi,
> > > >
> > > > You may need to give your normal user account read permission to that
> > > > directory.
> > > >
> > > > gmx solvant doesn't exist, of course, but I assume that was a typo!
> :-)
> > > >
> > > > Mark
> > > >
> > > > On Mon, May 18, 2015 at 6:58 AM Sanchaita Rajkhowa <
> > > srajkhowa18 at gmail.com>
> > > > wrote:
> > > >
> > > > > Dear all
> > > > >
> > > > > I followed the same steps to install Gromacs - 5.0.4 in ubuntu -
> > 14.04
> > > > > (64bit) and seems like things get installed but I am not able to
> get
> > > "gmx
> > > > > solvant" command.
> > > > >
> > > > > I have searched in my installation dir /soft/gmx504/bin/ and also
> > > "source
> > > > > /soft/gmx504/bin/GMXRC.bash" in my bashrc file.
> > > > >
> > > > > Kindly help.
> > > > >
> > > > > with regards
> > > > > Sanchaita
> > > > >
> > > > > On 14 May 2015 at 08:54, James Lord <jjamesgreen110 at gmail.com>
> > wrote:
> > > > >
> > > > > > Hi Saeed,
> > > > > > You don't necessarily need to install it first from Ubuntu
> software
> > > > > center
> > > > > > and then update it. you can directly get the latest version and
> > > follow
> > > > > the
> > > > > > instruction on gromacs website.
> > > > > > Quick and dirty installation
> > > > > > <
> > > > > >
> > > > >
> > > >
> > >
> >
> http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=command#TOC
> > > > > > >
> > > > > >
> > > > > >    1. Get the latest version of your C and C++ compilers.
> > > > > >    2. Check that you have CMake version 2.8.8 or later.
> > > > > >    3. Get and unpack the latest version of the GROMACS tarball.
> > > > > >    4. Make a separate build directory and change to it.
> > > > > >    5. Run cmake with the path to the source as an argument
> > > > > >    6. Run make, make check, and make install
> > > > > >
> > > > > > Or, as a sequence of commands to execute:
> > > > > >
> > > > > > tar xfz gromacs-5.0.5.tar.gz
> > > > > > cd gromacs-5.0.5
> > > > > > mkdir build
> > > > > > cd build
> > > > > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > > > > > make
> > > > > > make check
> > > > > > sudo make install
> > > > > > source /usr/local/gromacs/bin/GMXRC
> > > > > >
> > > > > > Cheers
> > > > > >
> > > > > > James
> > > > > >
> > > > > >
> > > > > > On Thu, May 14, 2015 at 1:53 PM, saeed poorasad <
> > > s_poorasad at yahoo.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Dear Gromacs users ,
> > > > > > > Greetings .I want to install Gromacs with using of UBUNTU
> > software
> > > > > center
> > > > > > > .  Now I want to know about updating process of this version of
> > > > gromacs
> > > > > > > . Does it update automatically with Ubuntu ?
> > > > > > > Thanks for your attention .Best,Saeed.
> > > > > > > --
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