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

[Mark Abraham]

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.Abraham at anu.edu.au
> <mailto: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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