bharat gupta bharat.85.monu at gmail.com
Tue Jan 18 04:50:54 CET 2011


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.. 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.. 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...

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110117/209da861/attachment.html>

More information about the gromacs.org_gmx-users mailing list