[gmx-users] minimization quagmire

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Wed Sep 15 13:07:52 CEST 2010

Hello everyone, 

I have a question regarding the results of minimization. I have two structures that are the same except for 2 residues in the core of the structure that have been changed from luecine to  to glycine. The leucine structure is very well packed and the core is hydrophobic. The introduction of two glycines in the center creates a a cavity in this hydrophobic region.
I had expected the leucine structure to have better(lower) energy after optimization, however, the opposite was true. I have run minimization in vacuum and with water (water enters the cavity) and the structure with glycine has better energy in both cases.

The minimization procedure is what I think is standard, the em 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              =  1000
;    Energy minimizing stuff
emtol               =  20
emstep              =  0.01

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

I am using gromacs on windows through cygwin. 

Thank you in advance for your help,
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