Hi Jason,
it is technically obvious that no positional restraints would help in
speeding up the calculations. At the same time, I have the following
related question: in a REMD simulation I should choose a number of
replicas roughly rpportional to the square root of the number of atoms
in the system. If I fix 'the rest of the protein', I'm dealing with
definitely less degrees of freedom sampled than if I'm leaving all the
residues free to move. So I would need to have less replicas to deal
with the part of the system. Am I correct? In case I leave everything
free the simulations seems to be to be not feasible at all...
To make it more clear, here is a short description of my system. I have
8 N-terminal residues, which are very flexible, whereas the 9th is a Cys
residue forming an S-S bridge. The rest of the protein starting from the
residue 9 has a well-defined stable protein core. My interest is to
study the conformations of the flexible N-terminus and not to describe
the motions of the whole protein, though for sure they are some way
definitely interconnected. In particular, I'm just interested in the
probability of some specific conformations of N-terminus.
Or maybe just a very long (let's say ~10 microseconds) classical
unrestrained MD simulation would be more appropriate to make such an
analysis?
Thanks a lot for your help and cheers,
Sergey
On 09/08/2015 10:15 PM, Jason Swails wrote:
> On Tue, Sep 8, 2015 at 10:05 AM, Sergey Samsonov <
> sergeys.biotec.tu-dresden.de> wrote:
>
>> 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.
>
> I would have naively expected it to be ~2x faster...
>
>
>
>> Applying a cut-off (cut
>> = 10) made it 1.5 times faster as well. This is already significant.
>>
> Yes, but a cutoff of 10 in a GB simulation is really quite horrible. The
> electrostatic interactions are far too long-range for 10 A to be a
> reasonable cutoff.
>
>> 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.
>>
> Well there are no computational performance implications of applying
> either position restraints or constraints.
>
> 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 Fri Sep 11 2015 - 00:30:03 PDT
