[gmx-users] interaction energy

[balaji nagarajan]

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 ? 


  

> 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
> 
> ========================================
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