[gmx-users] Gcc

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 24 11:09:20 CEST 2017 

Hi Joao, Anshul and all,

Let's all please remember to keep the environment friendly and professional.

That means not making assumptions about other people's intentions. Learning
complex things like simulation science take time, and people often make
mistakes when joining new communities, particularly if it's in a language
with which they are not fully familiar. :-)

That also means remembering that everybody here is volunteering their time
to help others, and asking only for some of that time when you really need
it is important if you wish to keep others motivated to help you. Look for
your own answers first!

Please all take a moment to review the thoughts at
http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)

Cheers,

Mark

On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> Dear Anshul,
>
> I thought by movie you meant that you wanted to visually check the
> trajectory. ​For PyMOL, google search "pymol movie" produces about 31.000
> results in 0,31 seconds. The first hit is exactly what you want:
>
> https://pymolwiki.org/index.php/MovieSchool
>
> My previous email will still be valid as you'll first need to make PyMOL
> read your trajectory.
>
> - - -
>
> I know you want the exact array of commands you need to input in order to
> get a movie done, but I will not do that. I believe it is better to provide
> the information from which you can learn on your own. It's a bit of the old
> "give a man a fish and you feed him for a day; teach a man to fish and you
> feed him for a lifetime" proverb. The fact you waited a full weekend
> instead of spending a couple of minutes searching and trying yourself tells
> me that you're most likely just interested in the "fish", but I'll stick to
> my belief that learning is better.
>
> /J
>
>
> On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> anshullahariya17 at gmail.com
> > wrote:
>
> > hello rahul,
> > can u tell me how to make movie??
> >
> >
> > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > joao.m.a.henriques at gmail.com> wrote:
> >
> > > ​Plus, installing multiple version of the same software (e.g. gcc) is
> not
> > > problematic at all *when done by someone that knows what he/she is
> > doing*.
> > > Furthermore, I completely disagree with Vytautas Rakeviius final
> advice.
> > It
> > > wouldn't cross anyone's mind to change OS in order to use a different
> gcc
> > > version. That is ludicrous. I obviously don't recommend that an
> > > inexperienced user should start compiling stuff blindly on their
> machine,
> > > but that is just plain bad practice and impractical.
> > >
> > > But I digress, this is not really GROMACS related.
> > >
> > > A nice weekend to everyone!
> > > João
> > >
> > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > joao.m.a.henriques at gmail.com> wrote:
> > >
> > > > You have (at the very least) three solutions regarding the movie:
> > > >
> > > > [1] Use gmx trjconv (see http://manual.gromacs.org/
> > documentation/5.1.4/
> > > > onlinehelp/gmx-trjconv.html) to generate a PDB file with the desired
> > > > trajectory frames. Load and play it in PyMOL et voilà!
> > > >
> > > > [2] Install the GROMACS plugin for PyMOL, which will allow you (among
> > > > other things) to directly read the trajectory files without having to
> > > > resort to gmx trjconv (see https://pymolwiki.org/index.
> > > php/GROMACS_Plugin
> > > > ).
> > > >
> > > > [3] Use VMD which can read GROMACS trajectory output files straight
> out
> > > of
> > > > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> > > >
> > > > For details regarding gmx trjconv please read the documentation. It
> is
> > > > fairly trivial and only you know exactly what system you have at
> hand.
> > > Some
> > > > options will vary depending on that.
> > > >
> > > > - - -
> > > >
> > > > Regarding gcc, depending on your operating system you can either use
> a
> > > > package manager to install the desired version of gcc or compile it
> > > > yourself. After installing it don't forget to make sure GROMACS knows
> > > where
> > > > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag when
> > > > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/c++).
> > > > These paths are obviously fictitious and need to be changed with the
> > > right
> > > > ones.
> > > >
> > > > Best regards,
> > > > João
> > > >
> > > > On Fri, Apr 21, 2017 at 10:47 AM, Anshul Lahariya <
> > > > anshullahariya17 at gmail.com> wrote:
> > > >
> > > >> okkk. it's fine...
> > > >>
> > > >>
> > > >> On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH <
> > drrahulsuresh at gmail.com>
> > > >> wrote:
> > > >>
> > > >> > I am out
> > > >> > Can I say that to u on Monday.) ?
> > > >> > On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> > > >> > anshullahariya17 at gmail.com>
> > > >> > wrote:
> > > >> >
> > > >> > > yes rahul, i use pymol but dont know how to make movie
> > > >> > >
> > > >> > >
> > > >> > > On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <
> > > >> drrahulsuresh at gmail.com>
> > > >> > > wrote:
> > > >> > >
> > > >> > > > You must use pymol
> > > >> > > >
> > > >> > > >
> > > >> > > > On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> > > >> > > > anshullahariya17 at gmail.com>
> > > >> > > > wrote:
> > > >> > > >
> > > >> > > > > thanks rahul
> > > >> > > > >
> > > >> > > > >
> > > >> > > > > and how to make md movie for 5ns by command.??
> > > >> > > > >
> > > >> > > > >
> > > >> > > > > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <
> > > >> > drrahulsuresh at gmail.com
> > > >> > > >
> > > >> > > > > wrote:
> > > >> > > > >
> > > >> > > > > > Yum apt-get gcc version
> > > >> > > > > > Yum update
> > > >> > > > > > Yum upgrade
> > > >> > > > > > Yum install
> > > >> > > > > >
> > > >> > > > > >
> > > >> > > > > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <
> > > >> > > mark.j.abraham at gmail.com
> > > >> > > > >
> > > >> > > > > > wrote:
> > > >> > > > > >
> > > >> > > > > > > Hi,
> > > >> > > > > > >
> > > >> > > > > > > That's a good question for google or the forums of your
> > > >> operating
> > > >> > > > > system,
> > > >> > > > > > > not here. :-)
> > > >> > > > > > >
> > > >> > > > > > > Mark
> > > >> > > > > > >
> > > >> > > > > > > On Thu, 20 Apr 2017 12:42 Anshul Lahariya <
> > > >> > > > anshullahariya17 at gmail.com>
> > > >> > > > > > > wrote:
> > > >> > > > > > >
> > > >> > > > > > > > hello,
> > > >> > > > > > > >
> > > >> > > > > > > > I want to change my gcc and want to install gcc
> version
> > > >> later
> > > >> > > than
> > > >> > > > 5.
> > > >> > > > > > > > what can i do so i can change the version of gcc to
> > > >> gcc-4.9.4
> > > >> > > > > > > > --
> > > >> > > > > > > > Gromacs Users mailing list
> > > >> > > > > > > >
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> > > >> > > > > > > --
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> > > >> > > > > > --
> > > >> > > > > > *Regards,*
> > > >> > > > > > *Rahul Suresh*
> > > >> > > > > > *Research Scholar*
> > > >> > > > > > *Bharathiar University*
> > > >> > > > > > *Coimbatore*
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> > > >> > > > --
> > > >> > > > *Regards,*
> > > >> > > > *Rahul Suresh*
> > > >> > > > *Research Scholar*
> > > >> > > > *Bharathiar University*
> > > >> > > > *Coimbatore*
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> > > >> > --
> > > >> > *Regards,*
> > > >> > *Rahul Suresh*
> > > >> > *Research Scholar*
> > > >> > *Bharathiar University*
> > > >> > *Coimbatore*
> > > >> > --
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