[gmx-developers] calculating poteintial energy into do_md()

francesco oteri francesco.oteri at gmail.com
Tue Jul 17 09:11:54 CEST 2012 

2012/7/16 Shirts, Michael (mrs5pt) <mrs5pt at eservices.virginia.edu>

> That sounds reasonable.  I think the plan will be, then:
>
> 4.6: a good explanation of how to set up REST2 using lambda values
>

I agree, but in my opinion you should say something regarding the
performance drop


>
> 5.0: an implementation of REST2 (or some variant -- why does it have to be
> sqrt(T_0/T_B) scaling that's best?)


I don't know. You shoul ask the authors :) I guess it is the most
convenient because when T_B=T_0
sqrt(T_0/T_B)  = 1 so you have an unmodified Hemiltonian, so you can use
this replica for data analysis


 that is just as fast as normal replica

> exchange simulations. It will probably still be build on the lambda
> machinery for ease of coding, but might be toggleable by a simple mdp
> switch.  If not, it will be well explained in the documentation.
>
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>
> > From: francesco oteri <francesco.oteri at gmail.com>
> > Reply-To: Discussion list for GROMACS development <
> gmx-developers at gromacs.org>
> > Date: Mon, 16 Jul 2012 19:50:13 +0200
> > To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> > Subject: Re: [gmx-developers] calculating poteintial energy into do_md()
> >
> > Hi Michael,
> > I agree with you respect the recoding. But performance difference is of
> 2x.
> > I started inserting the features in 4.5.5  thursday and within today or
> > tomorrow
> > I will end. I plan one day of debug. So totally 4-5gg...I will get back
> > these
> > days as performance improvement :)
> >
> > Of course, implementing seriously this features will take more time both
> > for coding
> > and testing. But right now I am not planning to do it seriously.
> >
> > Maybe later when 4.6 will be out and if it will give me problem.
> >
> >
> > 2012/7/16 Berk Hess <hess at kth.se>
> >
> >>  On 07/16/2012 06:08 PM, francesco oteri wrote:
> >>
> >>
> >>
> >> 2012/7/16 Berk Hess <hess at kth.se>
> >>
> >>>  Using lambda scaling for non-bonded interactions is going to be very
> >>> slow.
> >>>
> >>
> >>  If it is done with the actual implementation, you are right. But if
> >> mdrun recognize rest2=yes thzn it rescales the
> >> parameters at teh beginning. Then a normal MD run goes.
> >>
> >>
> >>>
> >>> But this would scale the protein-protein non-bonded interactions with
> >>> lambda^2.
> >>>
> >>
> >>
> >>  Why? computing charge-charge interaction is:
> >>
> >>  S*qi*S*qj = (S^2 )*qi*qj
> >> but S=sqrt(Bi/B)
> >> so what I obtain is:
> >> (Bi/B)* qi*qj
> >>
> >>  That is exactly what I want: rescaling by (Bi/B) protein-protein
> >> interactions
> >>
> >>   Ah, sorry, that works indeed.
> >>
> >> Cheers,
> >>
> >> Berk
> >>
> >>
> >>
> >>>  Is that what you want?
> >>>
> >>> Cheers,
> >>>
> >>> Berk
> >>>
> >>>
> >>> On 07/16/2012 05:06 PM, francesco oteri wrote:
> >>>
> >>> In the paper they just say that non bonded rescaling is obtained
> >>> rescaling
> >>> LG epsilon by Bi/B and the protein charges by sqrt(Bi/B).
> >>>
> >>>  I did simulation using the lambda approach and I qualitatively
> >>> reproduced
> >>> the results.
> >>>
> >>>  Just to give my contribution, I think the most efficient way to
> >>> implement REST2
> >>> is using the lambda approach as follows:
> >>>
> >>>  1) in .mdp introducing a new keyword like rest2 = yes/no
> >>> 2) using the init_lambda value to rescale the parameters at the
> bootstrap
> >>> of md
> >>>    (es. in do_md or init_replica_exchange).
> >>> 3) running the code as normal MD and swapping the states
> >>>
> >>>  Since point 1 implies modification of grompp and point 2 requires the
> >>> knowledge of
> >>> the data structure,  I am just implementing point 3 while point 2 is
> >>> demanded to external
> >>> scripts.
> >>>
> >>>  Francesco
> >>>
> >>> 2012/7/16 Berk Hess <hess at kth.se>
> >>>
> >>>> On 07/16/2012 04:42 PM, Shirts, Michael (mrs5pt) wrote:
> >>>>
> >>>>> One question, since better REST2 is one item on the todo list for
> 5.0,
> >>>>> and I
> >>>>> want to be thinking about the possibilities.
> >>>>>
> >>>>> For solute-solvent energy rescaling, how does one calculate the
> changes
> >>>>> in
> >>>>> solute-solvent energy without doing multiple PME calls to decompose
> the
> >>>>> electrostatic energy?
> >>>>>
> >>>>> I'm guessing that by since your are load multiple topologies of the
> >>>>> system,
> >>>>> for each of those topologies, you can explicitly write new nonbonded
> >>>>> pairwise parameter terms between the water and protein.  This is a
> pain
> >>>>> to
> >>>>> do (need new ij terms for every parameter pair) but straightforward
> in
> >>>>> the
> >>>>> end to automate.  Is this how your are planning to do it?
> >>>>>
> >>>>> Without PME, then it's straightforward to decompose into
> solute-solvent
> >>>>> energy / solute-solute / solvent-solvent electrostatics, though for
> >>>>> adding
> >>>>> long term to Gromacs, we'd want to support PME.
> >>>>>
> >>>>  No, even without PME this is not straightforward.
> >>>> Using a plain cut-off's for electrostatics is horrible, so I'd say you
> >>>> want to use reaction-field.
> >>>> But with reaction-filed the correction terms are non pair-wise, as
> with
> >>>> PME.
> >>>>
> >>>> Cheers,
> >>>>
> >>>> Berk
> >>>>
> >>>>>
> >>>>> Best,
> >>>>> ~~~~~~~~~~~~
> >>>>> Michael Shirts
> >>>>> Assistant Professor
> >>>>> Department of Chemical Engineering
> >>>>> University of Virginia
> >>>>> michael.shirts at virginia.edu
> >>>>> (434)-243-1821
> >>>>>
> >>>>>
> >>>>>    From: francesco oteri <francesco.oteri at gmail.com>
> >>>>>> Reply-To: Discussion list for GROMACS development <
> >>>>>> gmx-developers at gromacs.org>
> >>>>>> Date: Mon, 16 Jul 2012 16:13:16 +0200
> >>>>>> To: Discussion list for GROMACS development <
> >>>>>> gmx-developers at gromacs.org>
> >>>>>> Subject: Re: [gmx-developers] calculating poteintial energy into
> >>>>>> do_md()
> >>>>>>
> >>>>>> Hi
> >>>>>>
> >>>>>> 2012/7/16 Mark Abraham <Mark.Abraham at anu.edu.au>
> >>>>>>
> >>>>>>    On 16/07/2012 10:59 PM, francesco oteri wrote:
> >>>>>>>
> >>>>>>> Hi,
> >>>>>>> what I am trying to do is implementing the REST2 tecnique [1]
> >>>>>>> The goal is enanching the conforlational sampling splitting the
> >>>>>>> system in
> >>>>>>> two parts: solvent and solute.
> >>>>>>> The two groups have a different APPARENT temperature because the
> >>>>>>> bonded
> >>>>>>> interaction within the solute atoms are rescaled by a factor Bi/B (
> >>>>>>> Bi=1/Ti*Kb,  Ti = apparent temperature for the i-th replica,
> >>>>>>> B=Boltzmann
> >>>>>>> constant) and the  protein-water interactions are rescaled by
> >>>>>>> sqrt(Bi/B).
> >>>>>>> So the system temperature, regulated by the thermostat, is equal
> >>>>>>> along the
> >>>>>>> different replicas but the dynamic of the different replicas
> >>>>>>> changes becaus of the different Boltzmann factor.
> >>>>>>> To implement the tecnique, the naive approach (adopted in [2]) is:
> >>>>>>> 1) Generating N-different topology (N= number of replicas).
> >>>>>>> 2) Removing same check at the beginning of the Replica Exchange
> code,
> >>>>>>> in
> >>>>>>> order to run N replicas with equal run parameters (temperature,
> >>>>>>> pression,
> >>>>>>> ecc. ecc.)
> >>>>>>> 3) Changing the acceptance ratio formula.
> >>>>>>>
> >>>>>>>   This approach has been developped for gmx4.0.3 but I need to use
> >>>>>>> gmx4.5.5 because it has a native implementation of the CHARMM
> >>>>>>> force-field.
> >>>>>>> Since the code between the two versions is different I am trying to
> >>>>>>> figure
> >>>>>>> out how to reinvent the wheel.
> >>>>>>>
> >>>>>>>   As shown in [3] and adopted in [2] the same result can be
> obtained
> >>>>>>> using
> >>>>>>> the lamda dynamics in gromacs.In this case, only one topology has
> to
> >>>>>>> be
> >>>>>>> generated. The state A correspond to the replica at the lowest
> >>>>>>> apparent
> >>>>>>> temperature, while the state B represents the highest temperature
> >>>>>>> replica.
> >>>>>>> Intermediate replicas are generated changing the init_lambda value.
> >>>>>>>
> >>>>>>>   What has been found, this approach results in slowest run.
> >>>>>>>
> >>>>>>>
> >>>>>>>   So, right now I got stuck at the point 3. In fact  to find:
> >>>>>>>
> >>>>>>>   delta = B( Va(Xb) + Vb(Xa) - Va(Xa) - Vb(Xb))
> >>>>>>>
> >>>>>>>   I need to calculate Va(Xb) and Vb(Xa)
> >>>>>>>
> >>>>>>>
> >>>>>>> Va(Xb) is determined by the potential of replica a and the
> >>>>>>> coordinates of
> >>>>>>> replica b, so it is most effectively evaluated on the processor
> that
> >>>>>>> has
> >>>>>>> the coordinates of replica b. If the topology is the same at the
> >>>>>>> replicas a
> >>>>>>> and b, then can Va(Xb) be computed by replica b by rescaling
> suitably
> >>>>>>> the
> >>>>>>> quantities that contributed to Vb(Xb), based on the knowledge that
> >>>>>>> replica
> >>>>>>> a is the exchange partner? Then the quantities that are exchanged
> >>>>>>> before
> >>>>>>> the test are Va(Xb) and Vb(Xa). Should be as fast as regular REMD.
> >>>>>>>
> >>>>>>>
> >>>>>> This is my idea, indeed
> >>>>>>
> >>>>>>
> >>>>>>>
> >>
> >> --
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> >> gmx-developers at gromacs.org
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> >>
> >
> >
> >
> > --
> > Cordiali saluti, Dr.Oteri Francesco
> > --
> > gmx-developers mailing list
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-- 
Cordiali saluti, Dr.Oteri Francesco
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