On 8/04/2010 3:57 PM, shahid nayeem wrote:
Please see the following pr.mdp and full.mdp
pr.mdp
You're using plain cut-off electrostatics, which was last acceptable in
about 1958. :-)
Get your system simulating stably at room temperature using a sensible
electrostatics model before worrying about forcing unfolding at high
temperatures. Make sure you can walk before you try to run.
Mark
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 50000 ; total 100 ps.
nstcomm = 1
nstxout = 500
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein Non-protein
tau_t = 0.1 0.1
ref_t = 500 500
; Energy monitoring
energygrps = Protein Non-protein
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 500 K.
gen_vel = yes
gen_temp = 500.0
gen_seed = 173529
full.mdp
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 50000000 ; total 100000 ps.
nstcomm = 1
nstxout = 5000
nstvout = 40000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein Non-protein
tau_t = 0.1 0.1
ref_t = 500 500
; Energy monitoring
energygrps = Protein Non-protein
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 500 K.
gen_vel = no
gen_temp = 500.0
gen_seed = 173529
Please tell me why protein shows unfolding in very first frame.
msnayeem
On 4/7/10, *Mark Abraham* <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 7/04/2010 9:08 PM, shahid nayeem wrote:
Dear users
Please let me know some basic question. I am sorry if I am asking a
silly question.
a) While simulating a protein thermal unfolding at high
temperature say
500K should I run position restraint dynamics at 500k or at
298K. I am
doing 100ps position restraint dynamics at 500k. Am I right in
doing so.
The usual purpose of position restrained MD is to allow the system
to achieve close to the ensemble desired for the start of the
simulation without perturbing the initial structure.
b) While using Berendsen thermostat, how to select a value of
tau_t and
how does it affects simulation output. The same question for
NoseHoover
thermostat.
Start by reading the GROMACS manual sections.
c) After completing the 100ns simulation when I view the .xtc
file in
VMD I find that alpha helix of the protein is unfolded in very
first
frame collected at 10ps interval and reduced by trjconv at 50ps
interval. Is it possible. If not then where I am wrong.
I did Steepest descent minimization, then 100ps position restraint
Dynamics at 500K and then 100ns full dynamics at 500k.
10ps would be very fast for a lengthy helix to unfold, however
you've deliberately taken your force field out of the zone where it
was parameterized, so we can't really infer anything about its
behaviour. You could also have a broken model physics in your .mdp
file, but we can't know about that.
The real lesson here is not to do a lengthy simulation without
looking at the early and ongoing results.
Mark
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