On 18/01/2011 2:50 PM, bharat gupta wrote:
Hi,
I did the energy minimization of my protein (230 amino acids) after
adding ions .. and after checking the potential energy of the system I
was getting thee graph which is different from the one given in the
lysozyme tutorial i.e. the the potential line in graph is not parallel
to the x axix..
You're comparing apples and oranges... maybe lysozyme is already pretty
close to the minimum. Consider the axis scales, also. Note that the
energy change per EM step doesn't have any physical meaning.
Here is are conditions that I used for minimization :
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 50000
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
------------------------
I got the following result :-
Steepest Descents converged to Fmax < 2000 in 296 steps
Potential Energy = -6.9540075e+05
Maximum force = 1.9863752e+03 on atom 1669
Norm of force = 3.7864201e+01
------------------------------
I want to know which parameters are important to get a correct
minimized structure and what value do I have to take for emtol and
nsteps to minimize the structure properly.. Also how would I know that
at what value of emtol my protein will be minimized..
How long should a piece of string be? Your PE is OK, so if you reduce
emtol then you can reduce the maximum force. This will prolong the EM if
you think you need to do that.
I checked the manual to get some details but there only the basic
theory of minimzation is written.. A detailed explanation will be more
helpful...
The purpose of EM is normally to relieve bad contacts, fill solvent
voids, etc. Do something plausible (like you've done) and then try the
next step. If you get problems there, go back and do EM harder (among
other strategies)
Mark
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