[gmx-users] Minimization and torsion angles

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Mon Feb 7 16:47:45 CET 2011


I have an input structure with poor torsion angles and after minimization with gromacs (both steepest descent and congugate gradient) I found that they were not corrected. There is enough free space for the torsion angles to be corrected. 
(I am sure of this because when I run the same structure in Insight it is able to correct them. Both programs give very similar structures with the major difference being the torsion angles.)

Has this happened because Gromacs potentials do not penalize poor omega angles? Or have I done something wrong? (I have added by .mdp file at the end of the mail)
Is there a way besides applying a restraint to every torsion angle to induce Gromacs to correct them? 

Thank you in advance for you help,

;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES  
constraints         =  none
integrator          =  cg
nsteps              =  2000
;    Energy minimizing stuff
emtol               =  2
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1
rvdw                =  1
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

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