[gmx-users] energy-minimisation problem

[Justin Lemkul]

On 1/29/13 4:43 AM, SANTU BISWAS wrote:
> dear users,
>
>                I am performing an energy minimization of
> polypeptide(formed by 10-residues of alanine, lysine,leucine,glutamic
> acid ) in vacuum box by using
> Steepest Descent(initially) and then Conjugate Gradient methods in
> gromacs_4.5.5_doubleprecision
> using charmm-27 force field for all system.I saw that for lysine and
> alanine potential energy
> value is positive but for leucine and glutamic acid potential energy
> value is nagative for both energy-
> minimisation methods.
> I do not understand why this is happening.
>

How are you extracting this information?  You don't even have energygrps set in 
the .mdp file, so I'm not sure how you've got energies per amino acid, which are 
relatively useless numbers anyway.  In vacuo, you probably have a lot of 
unsatisfied interactions that would not occur in the condensed phase.  Positive 
potential energies can thus arise.  As long as the EM converged to an acceptable 
value of Fmax, that's what you should be most concerned with.

-Justin

> Input file for energy-minimisation is
>
> ;title                    =
> cpp                     = /lib/cpp
> ;include               =-I../top/
> define                  = -DFLEXIBLE
> ;         Input file
>
> integrator             =  cg
> nsteps                 =  10000
> pbc                      =  no
> ns_type                =  simple
> nstlist                   =  0
> rlist                       =  0
> rcoulomb               =  0
> rvdw                      =  0
>
> ;         Energy minimizing stuff
>
> emtol                   =  0.001
> emstep                 =  0.1
> nstcgsteep            =  10
>
> ---
> 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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