[gmx-users] Gcc

João Henriques joao.m.a.henriques at gmail.com
Mon Apr 24 11:23:34 CEST 2017 

Dear Mark and by extension Anshul,

I did make an assumption at the bottom of my previous email, and that was
uncalled for (despite having good intentions, but that doesn't change
anything). I apologize for that. That, however, does not overshadow the
fact that I provided Anshul with all the necessary information in a most
friendly, voluntary and professional way throughout three separate emails.

Best regards,
João

On Mon, Apr 24, 2017 at 11:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > > > >> > > > > > > >
> > > > >> > > > > > > > * Please search the archive at
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> > > > Users_List
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> > > > >> > > > > > > --
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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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> > > > >> > > >
> > > > >> > > --
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> > > > >> > >
> > > > >> > --
> > > > >> > *Regards,*
> > > > >> > *Rahul Suresh*
> > > > >> > *Research Scholar*
> > > > >> > *Bharathiar University*
> > > > >> > *Coimbatore*
> > > > >> > --
> > > > >> > Gromacs Users mailing list
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