[gmx-users] rotamers during minimization

[Justin A. Lemkul]

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
> 

-- 
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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

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