Re: [gmx-users] gromacs instillation

2019-04-11 Thread Ali Ahmed
Yes I'm using the quick and dirty Installation

On Thu, Apr 11, 2019 at 12:55 PM RAHUL SURESH 
wrote:

> Are you following the quick and dirty Installation or modify your
> compilation?
>
> On Thu 11 Apr, 2019, 11:20 PM RAHUL SURESH, 
> wrote:
>
> >
> >
> > On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,  wrote:
> >
> >> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes,
> each
> >> terminal I run source /usr/local/gromacs/bin/GMXRC to strat using
> gromacs.
> >> I kind of confused which one I should modify
> >>
> >
> > If that is your executable directory, then there is nothing to modify.
> > What error actually you get?
> >
> > Please try the command gmx_mpi after source command. (A wild guess)
> >
> > Thank you
> >
> >
> >
> >>
> >> On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:
> >>
> >> > when you open a new terminal you need to run " source" again, but you
> >> > probably know this by now
> >> > or
> >> > add the path to your /etc/.profile to make the change permanent
> >> >
> >> > Sent from Mailspring (
> >> >
> >>
> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn
> >> ),
> >> > the best free email app for work
> >> > On Apr 11 2019, at 1:45 am, Mark Abraham 
> >> wrote:
> >> > > Hi,
> >> > >
> >> > > Each shell you open needs to be told how to find GROMACS, per
> >> > >
> >> >
> >>
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
> >> > >
> >> > > Mark
> >> > > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed, 
> wrote:
> >> > > > Hello GMX users
> >> > > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
> >> > well.
> >> > > > I run: source /usr/local/gromacs/bin/GMXRC and checked the
> version,
> >> it
> >> > was
> >> > > > 2019.1.
> >> > > > When I open a new terminal and hit gmx, it says gromacs is
> currently
> >> > not
> >> > > > installed. You can install it by typing: sudo apt install gromacs.
> >> > When I
> >> > > > did it, the version became 5.1.2.
> >> > > >
> >> > > > Any idea how to solve it!
> >> > > > Thank you
> >> > > > Ali
> >> > > > --
> >> > > > 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-requ...@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-requ...@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-requ...@gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> --
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> posting!
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] gromacs instillation

2019-04-11 Thread RAHUL SURESH
Are you following the quick and dirty Installation or modify your
compilation?

On Thu 11 Apr, 2019, 11:20 PM RAHUL SURESH,  wrote:

>
>
> On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,  wrote:
>
>> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each
>> terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs.
>> I kind of confused which one I should modify
>>
>
> If that is your executable directory, then there is nothing to modify.
> What error actually you get?
>
> Please try the command gmx_mpi after source command. (A wild guess)
>
> Thank you
>
>
>
>>
>> On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:
>>
>> > when you open a new terminal you need to run " source" again, but you
>> > probably know this by now
>> > or
>> > add the path to your /etc/.profile to make the change permanent
>> >
>> > Sent from Mailspring (
>> >
>> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn
>> ),
>> > the best free email app for work
>> > On Apr 11 2019, at 1:45 am, Mark Abraham 
>> wrote:
>> > > Hi,
>> > >
>> > > Each shell you open needs to be told how to find GROMACS, per
>> > >
>> >
>> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
>> > >
>> > > Mark
>> > > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
>> > > > Hello GMX users
>> > > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
>> > well.
>> > > > I run: source /usr/local/gromacs/bin/GMXRC and checked the version,
>> it
>> > was
>> > > > 2019.1.
>> > > > When I open a new terminal and hit gmx, it says gromacs is currently
>> > not
>> > > > installed. You can install it by typing: sudo apt install gromacs.
>> > When I
>> > > > did it, the version became 5.1.2.
>> > > >
>> > > > Any idea how to solve it!
>> > > > Thank you
>> > > > Ali
>> > > > --
>> > > > 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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.
>>
>
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Re: [gmx-users] gromacs instillation

2019-04-11 Thread RAHUL SURESH
On Thu 11 Apr, 2019, 11:15 PM Ali Ahmed,  wrote:

> I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each
> terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs.
> I kind of confused which one I should modify
>

If that is your executable directory, then there is nothing to modify. What
error actually you get?

Please try the command gmx_mpi after source command. (A wild guess)

Thank you



>
> On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:
>
> > when you open a new terminal you need to run " source" again, but you
> > probably know this by now
> > or
> > add the path to your /etc/.profile to make the change permanent
> >
> > Sent from Mailspring (
> >
> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn
> ),
> > the best free email app for work
> > On Apr 11 2019, at 1:45 am, Mark Abraham 
> wrote:
> > > Hi,
> > >
> > > Each shell you open needs to be told how to find GROMACS, per
> > >
> >
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
> > >
> > > Mark
> > > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
> > > > Hello GMX users
> > > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
> > well.
> > > > I run: source /usr/local/gromacs/bin/GMXRC and checked the version,
> it
> > was
> > > > 2019.1.
> > > > When I open a new terminal and hit gmx, it says gromacs is currently
> > not
> > > > installed. You can install it by typing: sudo apt install gromacs.
> > When I
> > > > did it, the version became 5.1.2.
> > > >
> > > > Any idea how to solve it!
> > > > Thank you
> > > > Ali
> > > > --
> > > > 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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.
>
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Re: [gmx-users] gromacs instillation

2019-04-11 Thread Ali Ahmed
I see gmx excutable in /usr/local/gromacs/bin/ and I see GMXRC. Yes, each
terminal I run source /usr/local/gromacs/bin/GMXRC to strat using gromacs.
I kind of confused which one I should modify


On Thu, Apr 11, 2019 at 10:08 AM p buscemi  wrote:

> when you open a new terminal you need to run " source" again, but you
> probably know this by now
> or
> add the path to your /etc/.profile to make the change permanent
>
> Sent from Mailspring (
> https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn),
> the best free email app for work
> On Apr 11 2019, at 1:45 am, Mark Abraham  wrote:
> > Hi,
> >
> > Each shell you open needs to be told how to find GROMACS, per
> >
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
> >
> > Mark
> > On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
> > > Hello GMX users
> > > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was
> well.
> > > I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it
> was
> > > 2019.1.
> > > When I open a new terminal and hit gmx, it says gromacs is currently
> not
> > > installed. You can install it by typing: sudo apt install gromacs.
> When I
> > > did it, the version became 5.1.2.
> > >
> > > Any idea how to solve it!
> > > Thank you
> > > Ali
> > > --
> > > 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-requ...@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-requ...@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-requ...@gromacs.org.
>
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Re: [gmx-users] gromacs instillation

2019-04-11 Thread p buscemi
when you open a new terminal you need to run " source" again, but you probably 
know this by now
or
add the path to your /etc/.profile to make the change permanent

Sent from Mailspring 
(https://link.getmailspring.com/link/1554995165.local-f06b1bee-57af-v1.5.3-420ce...@getmailspring.com/0?redirect=https%3A%2F%2Fgetmailspring.com%2F=Z214LXVzZXJzQGdyb21hY3Mub3Jn),
 the best free email app for work
On Apr 11 2019, at 1:45 am, Mark Abraham  wrote:
> Hi,
>
> Each shell you open needs to be told how to find GROMACS, per
> http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation
>
> Mark
> On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:
> > Hello GMX users
> > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> > I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
> > 2019.1.
> > When I open a new terminal and hit gmx, it says gromacs is currently not
> > installed. You can install it by typing: sudo apt install gromacs. When I
> > did it, the version became 5.1.2.
> >
> > Any idea how to solve it!
> > Thank you
> > Ali
> > --
> > 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-requ...@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
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> mail to gmx-users-requ...@gromacs.org.
>

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Re: [gmx-users] gromacs instillation

2019-04-11 Thread Mark Abraham
Hi,

Each shell you open needs to be told how to find GROMACS, per
http://manual.gromacs.org/documentation/current/install-guide/index.html#getting-access-to-gromacs-after-installation

Mark

On Thu., 11 Apr. 2019, 05:09 Ali Ahmed,  wrote:

> Hello GMX users
> I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
> 2019.1.
> When I open a new terminal and hit gmx, it says gromacs is currently not
> installed. You can install it by typing:  sudo apt install gromacs. When I
> did it, the version became 5.1.2.
>
> Any idea how to solve it!
>
> Thank you
> Ali
> --
> 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-requ...@gromacs.org.
>
-- 
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Re: [gmx-users] gromacs instillation

2019-04-10 Thread Ali Ahmed
Dear Rahul,
Thank you for your answer. Yes, I did remove the old version and all its
dependencies.
Usually, I use these commands for installation

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

This time I got this error and tried several options with no luck


Thanks
Ali



On Wed, Apr 10, 2019 at 10:55 PM RAHUL SURESH 
wrote:

> Hi
>
> On Thu 11 Apr, 2019, 8:39 AM Ali Ahmed,  wrote:
>
> > Hello GMX users
> > I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> > I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it
> was
> > 2019.1.
> > When I open a new terminal and hit gmx, it says gromacs is currently not
> > installed.
>
> This means gromacs is not installed in the source directory. Simple., You
> will know where you have the gromacs executable. Just give that address in
> source. Or better set it in bash so you needn't go for source everytime.
>
> > You can install it by typing:  sudo apt install gromacs. When I
> > did it, the version became 5.1.2.
> >
>
> That's wrong procedure. If you want 2019 version then you got to start
> from scratch. Delete all you preexisting gromacs file and reinstall 2019
> Ver. Don't use apt-get.
>
> >
> > Any idea how to solve it!
> >
> > Thank you
> > Ali
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Re: [gmx-users] gromacs instillation

2019-04-10 Thread RAHUL SURESH
Hi

On Thu 11 Apr, 2019, 8:39 AM Ali Ahmed,  wrote:

> Hello GMX users
> I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
> I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
> 2019.1.
> When I open a new terminal and hit gmx, it says gromacs is currently not
> installed.

This means gromacs is not installed in the source directory. Simple., You
will know where you have the gromacs executable. Just give that address in
source. Or better set it in bash so you needn't go for source everytime.

> You can install it by typing:  sudo apt install gromacs. When I
> did it, the version became 5.1.2.
>

That's wrong procedure. If you want 2019 version then you got to start
from scratch. Delete all you preexisting gromacs file and reinstall 2019
Ver. Don't use apt-get.

>
> Any idea how to solve it!
>
> Thank you
> Ali
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[gmx-users] gromacs instillation

2019-04-10 Thread Ali Ahmed
Hello GMX users
I have installed gromacs 2019.1 on Ubuntu 16.04 and everything was well.
I run: source /usr/local/gromacs/bin/GMXRC and checked the version, it was
2019.1.
When I open a new terminal and hit gmx, it says gromacs is currently not
installed. You can install it by typing:  sudo apt install gromacs. When I
did it, the version became 5.1.2.

Any idea how to solve it!

Thank you
Ali
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