[gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration

[Mark Abraham]

On 05/03/11, Kavyashree M  <hmkvsri at gmail.com> wrote:
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> On Sat, Mar 5, 2011 at 12:22 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
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> > It is difficult to say for certain how OPLS should be used with MD, since it was originally designed for different software doing MC simulations.  I commonly see rlist=rcoulomb=rvdw=1.0 with vdwtype = cutoff and coulombtype = PME in the literature.
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> > During EM there are no temperatures.  Please consult some textbook material if this concept is foreign to you.
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>  I am sorry sir I meant during production MD run? sorry for the mistake.
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> > There is no single metric that, in isolation, will tell you if a simulation is equilibrated.  You have to look at many variables and judge for yourself. First, is the ensemble stable (temperature, pressure, energy, whatever else)? Then, is the protein structure stable (RMSD, radius of gyration, secondary structure, hydrogen bonds, many more)?  From your RMSD plots, I would not be convinced that either are fully equilibrated, as one is still trending upwards.  More generally, as I said, you can't simply judge the simulation based on one criterion.
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> The Temperature , kinetic, potential and total energy  had equilibrated (I mean they were oscillating about a mean value). My 
> doubt in that was this equilibration had reached right from the beginning which is surprising as it has to take some time for the 
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> eqilibration to occur. But radius of gyration was quite bad there was no such sign of such equilibration.
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Assessing equilibration of an observable requires observing for a great deal longer than the time scale of the intrinsic variability of that observable. Only then can you assess whether any change in the value of that observable can be regarded as a property of equilibrium, or an artefact during the journey toward equilibrium. Different observables have different such time scales - total energy equilibrates within a few tens of picoseconds normally and it is easy to observe convergence because the fluctuations are small compared with the value. The pressure might not take that much longer to equilibrate, but its large fluctuations make it harder to assess convergence. So you need to assess to which category Rg belongs.

Mark



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> > > 4. If MD is run on a protein which had intrinsic domain motion, how will that equilibrate during MD? i.e., how will the rmsd plot appear when it is equilibrated?
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> > Depends entirely upon the types of motions that are involved.  Domain motions are usually very slow, and you may not see such movement on the nanosecond time scale with conventional MD.  Normal modes calculations are generally better-suited for these types of studies.
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> > >     Will it equlibrate at all? will not the domain movement or movement of a large loop in the structure prevent it from equilibration?
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> > Ideally, in the limit of infinite sampling, you would see your protein's structure interconvert between whatever conformations are expected at some predictable time interval.  I doubt you'll ever be able to run a conventional simulation long enough to see such behavior for even the smallest protein domains, unless you spend several years collected many microseconds of data. You may be able to see such motion faster with implicit solvent, but then the kinetics are meaningless in an absolute sense.
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> Yes I got this point. Thanks. So the question here is, does the cut offs that i have chosen had given rise to such anomalies or any other major factor is there?
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> > -Justin
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> > -- 
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> > ========================================
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> > Justin A. Lemkul
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> > Ph.D. Candidate
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> > ICTAS Doctoral Scholar
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> > MILES-IGERT Trainee
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> > Department of Biochemistry
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> > Virginia Tech
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> > Blacksburg, VA
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> > jalemkul[at]vt.edu(http://vt.edu) | (540) 231-9080
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> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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> > ========================================
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> Thanking you 
> With Regards
> M. Kavyashree 
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