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