[gmx-users] Gromacs in UBUNTU

Mon May 18 12:56:58 CEST 2015

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.
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>