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