[gmx-users] Equilibration MD and E.M. problems

luca deriu lucaderiu77 at yahoo.it
Wed Oct 20 12:53:11 CEST 2004

Hi users,
I'm performing a md simulation of 2 spectrin (211
residues) and 100000 water molecules.This is what I
1)energy minimization of the protein with steepest
descendents (OK!!!!)
2)short equilibration md of the protein (200ps) 
3)solvatation of the sistem with genbox that generate
about 100000 water molecules (box size 9,7,100).
4)e.m. of the water with freezed protein. 
5)short equilibration md of the water  (PROBLEMS!!!)
6)long equilibration (1ns) of the full system
I'm trying to minimize the 100000 spc waters, but I
find always the same thing.   
Steepest descendents converged quickly after 17
steps.I think it's a very bad minimization.After I do
the mdrun and the error is the same: a water molecules
can not to be settled.I'm sure that my problem is the
Now I'm tryng the water minimization with l-bgfs
My big problem is the message:"WATER MOLECULE ... CAN
NOT TO BE SETTLED" during equilibration mdrun.What
does it means?
I'm doing something wrong?
I've seen that Fmax and Fnorm increas during
minimization.Is it strange?
My future porpouse it's the elongation of the protein
with AFM, then I can't use constraints.I'm fighting
since two week with points 4)5)6).
This is my parameter file for water minimization:

title               = 
cpp                 =  /lib/cpp
define              = 
constraints         =  none
integrator          =  steep (or l-bfgs)
nsteps              =  5000
energygrps          =  Protein SOL SO4
rlist               =  1
rcoulomb            =  1
rvdw                =  1
freezegrps          =  Protein SOL SO4
freezedim           =  Y Y Y N N N Y Y Y
;       Energy minimizing stuff
emtol               =  1000
emstep              =  0.001

And this is my parameter file for water md simulation:

title               =  
cpp                 = /lib/cpp
define              =
constraints         = none  
integrator          = md
dt                  = 0.001 
nsteps              = 50000; 50 ps!
nstxout             = 500
nstvout             = 500
nstlog              = 500
nstenergy           = 100
nstxtcout           = 2000
nstlist             = 5
xtc_grps            = Protein
energygrps          = Protein  SOL 
freezegrps          = Protein SO4
freezedim           = Y Y Y Y Y Y
rlist               = 1.0
rcoulomb            = 1.0
rvdw                = 1.0
tcoupl              = Berendsen
tc-grps             = Protein   SOL  SO4
tau_t               = 0.1 0.1 0.1
ref_t               = 300 300 300
gen-vel             = yes
gen-temp            = 300
gen-seed            = 173529
Can anyone help me? Every input will be appreciate.
Thank you.

Luca Deriu,
Politecnico di Milano,
lucaderiu77 at yahoo.it

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