[gmx-users] Simulation parameter problem about protein unfolding

Chen amethyst0 at 126.com
Mon Oct 18 06:03:25 CEST 2010

Hi All,

I met a problem when I try to unfold a protein using Gromacs, It seemed the protein cannot be totally unfolded!

The simulated system has one Engrailed Homeodomain (En) protein (a three helix bundle protein with 54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- used to neutralize the system in a 5.752(nm)^3 water BOX. I use the NTP ensemble with T=498K and P=26atm. The system has 1nm thick water in each side of the En protein, and the density of the system has been adjusted to0.829 g/cm3.

The simulation lasted 24ns. The helixes disappeared at about 4ns. And after that some beta sheet formed in the N terminal of the protein. However, the protein kept in a compact state during the 24ns simulation. The radius of gyration of the protein fluctuated around 1.1nm during the simulation.

I've also noticed similar simulation done by others. For example, David Becka and Valerie Daggett reviewed their En protein unfolding in paper "Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods 34 (2004) 112–120". The simulations were performed with ENCAD and ilmm, and used an 0.8nm cutoff range. And the ensemble they used is NVE as I know. A stretched unfolding state occurred at about 5ns in their 60ns simulation in 498K, with little helix structure.

I was wondering whether the difference is caused by using different MD software and force field, or by some wrong parameters in my .mdp file. I've also conducted another 18ns simulation, and the result is almost the same. I list he mdp file below. Any comment is appreciated!


integrator               = md
dt                       = 0.002
nsteps                   = 3000000
nstxout                  = 500
nstvout                  = 500
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 1000

energygrps               = protein non-protein

nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0

coulombtype              = PME
rcoulomb                 = 1.0
vdwtype                  = cut-off
rvdw                     = 1.4
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4
ewald_rtol               = 1e-5
optimize_fft             = yes

tcoupl                   = v-rescale
tc_grps                  = protein non-protein
tau_t                    = 0.1  0.1
ref_t                    = 498  498
Pcoupl                   = Parrinello-Rahman
pcoupltype               = isotropic
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 26.0

gen_vel                  = yes
gen_temp                 = 498
gen_seed                 = 173529

constraints              = hbonds
lincs_order              = 10
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