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

Kavyashree M hmkvsri at gmail.com
Sat Mar 5 07:11:23 CET 2011

On Sat, Mar 5, 2011 at 12:22 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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.
> During EM there are no temperatures.  Please consult some textbook material
> if this concept is foreign to you.
 I am sorry sir I meant during production MD run? sorry for the mistake.

> 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.
> 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
eqilibration to occur. But radius of gyration was quite bad there was no
such sign of such equilibration.


>  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?
> 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.
>     Will it equlibrate at all? will not the domain movement or movement of
>> a large loop in the structure prevent it from equilibration?
> 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.
> 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?

> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Thanking you
With Regards
M. Kavyashree
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