Good suggestions from Tom; I'm also a little puzzled looking at the second
image at how the folded protein could fit in a water box that small.
Something looks off. As Tom said, look at how you built and equilibrated
the system.
On Jan 8, 2015 1:13 PM, "Thomas Cheatham" <tec3.utah.edu> wrote:
>
> > I wanted to run MD simulation for a protein in a TIP3P water box with
> > average 7100 atoms for 30 ns with step length of 0.001 ps. I am using
> NPT
> > ensemble with Langevin dynamics and periodic boundary conditions.
>
> Wow, that is an impressive unfolding event and one that likely occurs
> faster than is even possible in nature... Suggests some imbalance in the
> force (Luke).
>
> An input file alone is difficult to fully interpret without context. How
> was the coordinate/topology built? (e.g. what force field, what initial
> coordinates?). How was the system equilibrated prior to straight /
> production MD? Did you do initial minimization and then some initial MD
> to get the pressure/density to relax?
>
> Let's look at the mdin file...
>
> > I have the following control file !
> > imin=0, nmropt=0,
> > ntx=5, irest=1, ntrx=1,
>
> Restart from what? Did the initial temperature reported in the mdout look
> reasonable?
>
> > ntxo=1, ntpr=100, ntwr=100,
> > iwrap=1, ntwx=100, ntwv=0, ntwe=0,
> > ioutfm=0, ntwprt=0, idecomp=0,
>
> We recommend using NetCDF for trajectories for better precision, ioutfm=1,
> however this is not the source of the problem.
>
> > ntf=2, ntb=2, igb=0, nsnb=1,
>
> Constant pressure, periodic, but updating the pairlist every step?
> nsnb=1 ? Not recommended, since costly, but fortunately, this is ignored
> since ntb>1
>
> In general, only specify a parameter in the mdin file if you really want
> to set or change it; otherwise, let the default values help you... In
> other words, only chose variables to specify that you really want to set
> to values you control.
>
> > ipol=0, gbsa=0, iesp=0,
> > dielc=1.0, cut=10.0, intdiel=1.0,
>
> cut=10.0 is overkill, but not a problem. Makes the calculation a little
> slower. Could set cut=9 or 8
>
> > ibelly=0, ntr=0,
> > nstlim=5000, nscm=500, nrespa=1,
> > t=0.0, dt=0.001, vlimit=20.0,
>
> Why 1 fs time step instead of 2 fs? Did it previously blow up with a 2 fs
> time step? TIP3P is fine with 2 fs under normal conditions.
>
> > ntc=2, jfastw=0, tol=0.00001,
> > Tempi=310.0 , Temp0=310.0 , ntt=3, tautp=0.5, gamma_ln=2,
> > pres0=1.0, ntp=1, taup=2,
>
> Seems OK, however why 310K? Initial velocity is ignored since you are
> doing a restart. What was the initial temperature when you restarted
> (printed at step 100)?
>
> > However through the data analysis of the 30, I found that the protein
> > underwent complete unfolding leaving the water box although the boundary
> > conditions. Kindly find the attached snapshofts of the protein before and
>
> It cannot leave the boundary conditions, it can span across multiple boxes
> which if you visualized periodic images, you would see...
>
> > after complete unfolding. what do you think the source of error in my
> > simulation or control file ? I can support all the information that might
>
> As is often said on this list, look at the beginning of the simulation.
> Maybe even do a short simulation dumping information every step and see if
> the initial energies, temperatures, densities, etc are "reasonable".
>
> I have run a lot of simulations and never seen a protein or nucleic acid
> in solution "unfold" this fast; it is likely not the mdin, unless I am
> missing something but either the force field or coordinates/velocities.
>
> --tec3
>
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Received on Wed Jan 07 2015 - 20:30:03 PST
