[gmx-users] Gcc

João Henriques joao.m.a.henriques at gmail.com
Mon Apr 24 10:39:12 CEST 2017 

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
> > >> > > > > > > >
> > >> > > > > > > > * Please search the archive at
> > >> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-
> > Users_List
> > >> > > before
> > >> > > > > > > > posting!
> > >> > > > > > > >
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> > >> > > > > > > >
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> > >> > > > > > > >
> > >> > > 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
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> > >> > > > > > > posting!
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> > >> > > > > > --
> > >> > > > > > *Regards,*
> > >> > > > > > *Rahul Suresh*
> > >> > > > > > *Research Scholar*
> > >> > > > > > *Bharathiar University*
> > >> > > > > > *Coimbatore*
> > >> > > > > > --
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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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