[gmx-users] interaction energy

[Justin A. Lemkul]

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

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