[gmx-users] Gcc

Anshul Lahariya anshullahariya17 at gmail.com
Mon Apr 24 13:27:51 CEST 2017 

Dear Joao,

U r right, it's my fault, but the thing is that i was tried lot of thing
but not found anything perfect. That's by , i was waiting from weekend for
one answer.

Regards,
Anshul

On Mon, Apr 24, 2017 at 2:53 PM, João Henriques <
joao.m.a.henriques at gmail.com> wrote:

> 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
> > > > > >> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-
> > > > > Users_List
> > > > > >> > > before
> > > > > >> > > > > > > > posting!
> > > > > >> > > > > > > >
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> > > > > >> > > > > > > >
> > > > > >> > > > > > > --
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> > > > > >> > > > > > --
> > > > > >> > > > > > *Regards,*
> > > > > >> > > > > > *Rahul Suresh*
> > > > > >> > > > > > *Research Scholar*
> > > > > >> > > > > > *Bharathiar University*
> > > > > >> > > > > > *Coimbatore*
> > > > > >> > > > > > --
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> > > > > >> > > > > >
> > > > > >> > > > > --
> > > > > >> > > > > Gromacs Users mailing list
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> > > > > >> > > > > * Please search the archive at
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> > > > > >> > > > >
> > > > > >> > > > --
> > > > > >> > > > *Regards,*
> > > > > >> > > > *Rahul Suresh*
> > > > > >> > > > *Research Scholar*
> > > > > >> > > > *Bharathiar University*
> > > > > >> > > > *Coimbatore*
> > > > > >> > > > --
> > > > > >> > > > Gromacs Users mailing list
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> > > > > gmx-users
> > > > > >> or
> > > > > >> > > > send a mail to gmx-users-request at gromacs.org.
> > > > > >> > > >
> > > > > >> > > --
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> > > > > >> > >
> > > > > >> > --
> > > > > >> > *Regards,*
> > > > > >> > *Rahul Suresh*
> > > > > >> > *Research Scholar*
> > > > > >> > *Bharathiar University*
> > > > > >> > *Coimbatore*
> > > > > >> > --
> > > > > >> > Gromacs Users mailing list
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> > > > > >>
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