[gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat

[shahid nayeem]

Please see the following pr.mdp and full.mdp
pr.mdp


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.Abraham at 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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