Hi Jason,
thanks a lot for your help! Indeed, using HMR with dt = 0.004 for my
protein (132 aa) increased the speed 1.5 times. Applying a cut-off (cut
= 10) made it 1.5 times faster as well. This is already significant.
Yes, the reason why I wanted to restrain the rest of the protein is that
I didn't want to have significant deviations from the crystal structure,
which could lead to unfolding of the protein. But definitely I'll try
both with and without restraints to see how the global concerted motions
at longer timescales can be affected by such restraints.
Thanks and cheers,
Sergey
On 09/08/2015 01:29 PM, Jason Swails wrote:
> 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
>
--
Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax: (+49) 351 463 402 87
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
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Received on Tue Sep 08 2015 - 07:30:04 PDT
