[gmx-users] invacuo minimization

anwar at cdfd.org.in anwar at cdfd.org.in
Thu Sep 7 16:12:56 CEST 2006

Dear gmx users,
When I am minimizing a trimer protein in vacuum by SD as well as CG methods, 
one of the monomer gets apart from the rest of the protein and places itself 
away from the other two monomers, which are intact. No periodic box is 
assigned. But when I am running editconf and assigning a box, then the 
structures are intact. What is the reason for the above behaviour? 
I am pasting the em.mdp below:

cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
;integrator          =  CG
integrator          =  steep
nsteps              =  1000
;       Energy minimizing stuff
emtol               =  100
;for SD
emstep              =  0.1
;for CG
;emstep              =  0.001

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no


Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Hyderabad-500 076
Tel: +91-8413-235467,68,69,70 ext 2019
anwar.m1 at gmail.com


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