[gmx-users] interaction energy

[Justin A. Lemkul]

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: jalemkul at vt.edu
>  > To: gmx-users at 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: jalemkul at vt.edu
>  > > > To: gmx-users at 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
>  > > >
>  > > > ========================================
>  > > > --
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>  > >
>  >
>  > --
>  > ========================================
>  >
>  > 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 at 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!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to gmx-users-request at gromacs.org.
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> 

-- 
========================================

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

========================================