we discussed many of these issues some time ago so the ideas in this paper
might be of interest to people following this thread:
Modified Replica Exchange Simulation Methods for Local Structure Refinement
Xiaolin Cheng <
http://pubs.acs.org/action/doSearch?ContribStored=Cheng%2C+X>
,† <
http://pubs.acs.org/doi/abs/10.1021/jp045437y#jp045437yAF2> Guanglei
Cui <
http://pubs.acs.org/action/doSearch?ContribStored=Cui%2C+G> ,†
<
http://pubs.acs.org/doi/abs/10.1021/jp045437y#jp045437yAF2> Viktor Hornak
<
http://pubs.acs.org/action/doSearch?ContribStored=Hornak%2C+V> ,‡
<
http://pubs.acs.org/doi/abs/10.1021/jp045437y#jp045437yAF3> and Carlos
Simmerling
<
http://pubs.acs.org/action/doSearch?ContribStored=Simmerling%2C+C> †
<
http://pubs.acs.org/doi/abs/10.1021/jp045437y#jp045437yAF2>‡
<
http://pubs.acs.org/doi/abs/10.1021/jp045437y#jp045437yAF3>*
<
http://pubs.acs.org/doi/abs/10.1021/jp045437y#jp045437yAF1>
Department of Chemistry and Center for Structural Biology, Stony Brook
University, Stony Brook, New York 11794-3400
J. Phys. Chem. B, 2005, 109 (16), pp 8220–8230
*DOI: *10.1021/jp045437y
On Fri, Sep 11, 2015 at 3:11 AM, Sergey Samsonov <
sergeys.biotec.tu-dresden.de> wrote:
> 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 - 04:30:04 PDT
