Thank you very much for this valuable info! It is exactly what I was
looking for.
Is there an implementation of PREMD or LREMD available within AMBER14? I
searched through Amber Mailing List and I found the following discussion
about this from 2011: http://archive.ambermd.org/201104/0106.html
However, in LES manual it is stated that 'Sander can't currently
maintain groups of particles at different temperatures'. Does it mean
that the mentioned by Jason funtionality "/This functionality IS in
amber11 (and I'm guessing amber10 as well, but I'm //not certain about
that). It's accessed via -rem 2 with sander.LES.MPI. /" is not here
anymore or it is here but not documented explicitly?
Is it roughly correct how I understand the principal differences of REMD
and LES for my system: for my purpose (to analyze different
conformational states), REMD is more appropriate because it samples the
conformational space extensively, whereas just applying LES would rather
give me a fast way to reach a global energy minima (which is not what
I'm aiming to)?
Thank you very much for your help,
cheers,
Sergey
On 09/11/2015 01:25 PM, Carlos Simmerling wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
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--
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 - 08:00:03 PDT
