[gmx-users] water equilibration error

[luca deriu]

Hi users,
I'm trying to do how you said me, but I find always
the same error:water molecules cannot to be
settled.Now my way is:
1)E.M. of the spectrin in vacuum (first with steepest
descendent then with L-BFGS)
2)Solvatation of the system with genbox (using
-heavyh).There are 37000 SPC water.
3)E.M.of the full system
4)Short equilibration MD (200ps) with protein
restraints (define = -DPOSRES)
At 24ps appears the error message.
I thonk I'm doing right and I can't find what's wrong!
Now I'll try to restart the simulation but I think
it'll be the same thing.
Anyone can help me?
This is my mdp file for water equilibration:      
title               =  
cpp                 = /lib/cpp
define              = -DPOSRES 
integrator          = md
constraints         = all-bonds
dt                  = 0.002  
nsteps              = 100000; 200 ps!
nstxout             = 1000
nstvout             = 1000
nstlog              = 1000
nstenergy           = 100
nstxtcout           = 2000
pbc                 = xyz
ns_type             = grid
xtc_grps            = Protein
energygrps          = Protein  SOL 
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
Pcoupl              = no
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
gen-vel             = yes
gen-temp            = 300
gen-seed            = 173529
 
Thank you for any suggestion.
Luca Deriu
lucaderiu77 at yahoo.it


		
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