[gmx-users] rotamers during minimization

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Thu Feb 10 19:14:01 CET 2011

I would like to know if gromacs is designed to try and keep as close to the original structure as much as possible? 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. 
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/cppdefine              =  -DPOSRES  constraints         =  noneintegrator          =  steepnsteps              =  2000;; Energy minimizing stuff:;emtol               =  0.2emstep              =  0.001
nstcomm             =  1ns_type             =  gridrlist               =  1rcoulomb            =  1rvdw                =  1Tcoupl              =  noPcoupl              =  nogen_vel             =  no 		 	   		  
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