[gmx-users] unfolding a protein
Dastmalchi.s at tbzmed.ac.ir
Wed Feb 20 16:23:00 CET 2008
Thanks for the comments. Yes, I am showing MD ~.mdp file and I know that my system is not neutral. I am not following the unfolding path and my intention by unfolding the protein is to get a conformation which I could regard it as one of the feasible unfolded conformations.
Do you think, not neutralizing the system will somehow prevent unfolding?
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Wed 2008/02/20 06:35 ب.ظ
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] unfolding a protein
Quoting Siavoush Dastmalchi <Dastmalchi.s at tbzmed.ac.ir>:
> Hi there,
> I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide
> bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form
> and it didn't unfold. I know it may need longer time, but it doesn't show any
> sign of even starting to unfold. I think I am restraining the protein in some
> way. Please see below the content of ~.mdp file that I use.
My guess is that 1 ns is far too short to see any signs of unfolding.
Typically, we think of protein folding on the microsecond - second timescale,
so even if you speed things along by running your simulation at higher
temperature, you should be running tens of nanoseconds, if not 100 or more.
Check the literature to see what other people consider a reasonable time scale.
Also, what have you done in terms of minimization and equilibration? Are you
showing the production MD .mdp file?
As far as "thinking" you are restraining your protein, these are things you need
to be very sure of :-) Your topology likely specifies #include "posre.itp" if
you include a "define" statement within your .mdp file (which I don't see), so
I doubt you are restraining your protein in any way.
> Would you please let me know how I could unfold a protein using an MD
> Do you think unfolding a water soluble protein in vacuum would be faster?
Maybe, but what would it prove?
As a side note, are you including counterions in your simulation? I don't see
them incorporated into your tc-grps, so I'm wondering if you have an
> Cheers, Siavoush
> cpp = /lib/cpp
> include = -I../top
> integrator = md
> dt = 0.002
> nsteps = 500000
> nstxout = 1000
> nstvout = 1000
> nstlog = 100
> nstenergy = 100
> nstxtcout = 100
> xtc_grps = protein sol
> energygrps = protein sol
> nstlist = 10
> ns_type = grid
> rlist = 0.8
> coulombtype = cut-off
> rcoulomb = 1.4
> rvdw = 1.4
> pbc = xyz
> tcoupl = berendsen
> tc-grps = protein sol
> tau_t = 0.1 0.1
> ref_t = 400 400
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> gen_vel = yes
> gen_temp = 400
> gen_seed = 173529
> constraints = all-bonds
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul at vt.edu | (540) 231-9080
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