balaji nagarajan wrote:
Dear users !
thanks for the reply
I was able to do that , otherwise we can select the number of the option
one by one and enter then after that if we leave a empty line and
enter it gives all the needed energy terms !
my intension is not to do like this
is it possible to give it along the
g_energy
like
g_energy -f em.edr --- ( any options can be given along with this ,
i tried
g_energy -f em.edr 11 0 ( it is not working )
how it can be done ?
http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive
-Justin
> Date: Fri, 1 Jul 2011 13:53:59 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] interaction energy
>
>
>
> balaji nagarajan wrote:
> >
> >
> >
> > Dear Users !
> >
> > i would like to do this to a set of files !
> > so how to print the required values in the text mode or is there any
> > flag for this in
>
> I quoted the help description for how to do this. Is there some
problem? For
> instance, if you want to write the potential energy to an .xvg file,
type:
>
> 11 0
>
> and hit Enter. The values will be printed.
>
> -Justin
>
> > g_energy ,
> >
> > thanks in advance
> >
> >
> > > Date: Fri, 1 Jul 2011 13:40:28 -0400
> > > From: jalem...@vt.edu
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] interaction energy
> > >
> > >
> > >
> > > balaji nagarajan wrote:
> > > > Dear Users !
> > > >
> > > > Now i am able to do the protein solvent interaction !
> > > >
> > > > thanks ! i have understood !
> > > >
> > > > when i used the energygrps ,
> > > > when i used the
> > > > g_energy -f em.edr
> > > >
> > > > this command it prints all terms and asks to make selection as
below,
> > > >
> > > > 1 Bond 2 Angle 3 Proper-Dih. 4
> > > > Ryckaert-Bell.
> > > > 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR)
> > > > 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure
> > > > 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
> > > > 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
> > > > 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
> > > > 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
> > > > 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
> > > > 33 Mu-Y 34 Mu-Z
> > > > 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein
> > > > 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein
> > > > 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL
> > > > 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL
> > > > 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL
> > > > 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL
> > > > 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL
> > > > 49 LJ-14:SOL-SOL 50 T-rest
> > > >
> > > > -------------------------------------------------------
> > > >
> > > > how one can write this all to a file !
> > > >
> > >
> > > As prompted by g_energy:
> > >
> > > "Select the terms you want from the following list by
> > > selecting either (part of) the name or the number or a combination.
> > > End your selection with an empty line or a zero."
> > >
> > > Writing all terms to the same output file will result in nothing
but an
> > > incoherent mess. Choose terms wisely based on what you actually need
> > to analyze.
> > >
> > > -Justin
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > --
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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