[gmx-users] parts of protein unfolds during MD simulations

[jayant james]

Hi!
I have an issue with my protein modelling. I find that some of the helices
(not all) have greatly unfolded during a 8ns distance restrained MD run. I
am using the parameters below for the MD run. Is there any thing that can
treat the system better than PME?
thanks
Jayant James

title               =  Yo
cpp                 =  /usr/bin/cpp
define              = -DDISRES
constraints         =  none
;constraint_algorithm =  lincs
;lincs_order         =  4
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  1000000  ; total 1.0ns.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  5000
nstlog              =  5000
nstenergy           =  500
nstlist             =  10
ns_type             =  grid
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
disre               =  simple
disre_weighting     =  equal
; Berendsen temperature coupling is on in two groups
Tcoupl              =  V-rescale
tc-grps             =  tnc Non-Protein tnt NMR tni
tau_t               =  0.1 0.1 0.1 0.1 0.1
ref_t               =  300 300 300 300 300
; Energy monitoring
energygrps          = Protein Non-Protein
;tnc Non-Protein tnt NMR tni
; Pressure coupling is not on
Pcoupl              =  parrinello-rahman
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
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