abdullah ahmed wrote:
Hello,
I would like to know if gromacs is designed to try and keep as close to
the original structure as much as possible?
All motions are governed by the potential energy functions for bonded and
nonbonded interactions. Gromacs is not biased towards keeping certain
configurations. EM generally does not make very large changes, and is designed
only to optimize a structure such that it can be used stably during MD. Since
you're not dealing with any velocities, motions are generally very small.
After minimizing a structure with phenyl-alanines I realized that a
better minimization could be achieved if the rotamer had been changed
during the minimization. However I have been unable to induce gromacs to
do this on its own during minimization.
I could of course, change the original structure but I prefer not to.
If EM converged to acceptable criteria, then there's no problem. But you seem
to think that a certain structure is "better," so you should do whatever
achieves your goals and is scientifically sound. If a particular rotamer truly
is better, the structure should (in theory) adopt this position more often than
not during MD.
-Justin
Thank you in advance,
Abdullah Ahmed
My .mdp file is as follows:
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
;
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 2000
;
; Energy minimizing stuff:
;
emtol = 0.2
emstep = 0.001
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1
rvdw = 1
Tcoupl = no
Pcoupl = no
gen_vel = no
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
