jayant james wrote:
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?
In general, no.
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
Only an unusual system would be treated well by five different
temperature coupling groups. Temperature coupling algorithms work well
in conditions that resemble thermodynamic limits - large groups of atoms
with homogeneous heat capacity.
Mark
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
------------------------------------------------------------------------
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