[gmx-users] energy-mimisation-problem

[Justin Lemkul]

On 1/9/13 12:20 PM, SANTU BISWAS wrote:
> dear users,
>
>                I am performing an energy minimization of
> apolypeptide(formed by alanine-10-residues) in vacuum box by using
> Steepest Descent(initially) and then Conjugate Gradient methods in
> gromacs_4.5.5_doubleprecision.The chain length of
> alanine-10-mer is around 1.5 nm.Here i want to see only the sort-range
> interactions.so i use cutoff 2.0 nm .But in the
> output (.log )file there is a contribution of energy for long-range
> interactions(in both energy minimisation methods).
> I do not understand why this is happening.
>
> the input file for energy minimisation is,
>
> ;title                    =
> cpp                      = /lib/cpp
> ;include                  =-I../top/
> define                   = -DFLEXIBLE
> ;         Input file
> integrator              =  steep/cg
> nsteps                  =  10000
> nstlist                 =  1
> rlist                   =  1.0
> rcoulomb                =  2.0
> rvdw                    =  2.0
> ;         Energy minimizing stuff
> emtol                   =  0.001
> emstep                  =  0.1
> nstcgsteep              =  10
>
>

You haven't set a value for the pbc keyword, so it takes the default value 
(xyz).  The result is that you're not really minimizing in vacuo, but rather in 
some sort of pseudo-crystal state that probably has lots of periodicity 
artifacts.  That's probably the source of the energy terms - your peptide 
interacting with itself.

-Justin

> the output(.log )file is,
>
>   Energies (kJ/mol)
>             Bond          Angle            Proper Dih.
> Ryckaert-Bell.          LJ-14
>      8.48244e+00    2.10205e+01    2.39409e+00           9.86941e+01
>       1.47894e+02
>       Coulomb-14        LJ (SR)        LJ (LR)          Coulomb (SR)
> Coulomb (LR)
>      1.63221e+03   -1.64038e+02   -4.97232e-01   -3.00455e+03   -1.00138e+01
>        Potential       Pressure (bar)
>     -1.26841e+03    0.00000e+00
>
> ........
> santu
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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