[gmx-users] position_restraint anfd full Dynamics and berendsen Nose hoover Thermostat
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Apr 8 08:19:29 CEST 2010
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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