On Tue, Sep 8, 2015 at 3:50 AM, Sergey Samsonov <
sergeys.biotec.tu-dresden.de> wrote:
> Dear AMBERs,
>
> I have the following question: I'd like to study the conformational
> behaviour of a part of a system, in particular, several terminal
> residues of the protein, which are especially flexible. My idea is to
> restraint the rest of the system after a minimization and to let the
> terminus of interest to move in a REMD simulation in implicit solvent.
> What would be the most efficient and most appropriate way to apply
> restraints for the rest of the system? I checked already that it works
> with ntr=1 and restraintmask applied to the part of the system I don't
> want to let move, but it is pretty slow, and I wonder if there is a
> better way to carry out such calculations.
The issue is that regardless of the approach you take here, you still have
to do the full nonbonded energy calculation which requires a double-loop
over all pairs of atoms. That is the rate-limiting step, and there is
nothing you can do to avoid it unless you make approximations (like using a
shorter cutoff, which you can only do with the CPU code).
And by fixing part of the system in place, you potentially eliminate long
timescale, correlated motions between the flexible tail and the rest of the
system, so I question the utility of fixing part of the system (unless GB
tends to denature its native structure, in which case why would it
necessarily treat the flexible terminus correctly?
One feature to look into, potentially, is hydrogen mass repartitioning if
you want to increase the simulation efficiency, as that allows you to take
a timestep twice as long as normal (e.g., using SHAKE, HMR, and a 4 fs
timestep).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 08 2015 - 05:00:03 PDT
