Compare to the published benchmarks to see if it's ok. Hard to directly
compare explicit to implicit,, since cutoffs likely quite different.
On Jul 17, 2014 12:34 PM, "James Starlight" <jmsstarlight.gmail.com> wrote:
> some additional questions:
> 1) I've noticed low performance in case of the GPU-simulation of my system
> with the GB
>
> | Average timings for all steps:
> | Elapsed(s) = 26775.49 Per Step(ms) = 13.37
> | ns/day = 12.92 seconds/ns = 6687.18
>
> the same performance I have with the computation in explicit membrane-water
> solvent for the same system. Does something wrong with CUDA simulation and
> gb models?
>
> 2) in case of the usage of AMD with gb models how implicit solvent should
> be taken into account in the computation of the total boost (where the
> total number of atoms is used for the alpha and Ethreshold computation)
>
>
> TFH,
>
> James
>
>
> 2014-07-17 18:01 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>
> > yes,
> >
> > but in my case no posres are applied on loops so I could prevent the
> > rotation along peptide bond during its refirement with amd or other
> energy
> > boost added method.
> >
> > James
> >
> >
> > 2014-07-17 14:00 GMT+02:00 Carlos Simmerling <
> carlos.simmerling.gmail.com>
> > :
> >
> > The amber gb models don't support membranes or dual dielectric regions.
> You
> >> could look into work by others like wonpil im.
> >>
> >> - there is no box, so volume is infinite and pressure not really
> defined.
> >> -if the positional restraints are strong, no dihedral restraints should
> be
> >> needed. You can add them, or just check as the run proceeds to make sure
> >> those atoms aren't moving.
> >> On Jul 17, 2014 7:50 AM, "James Starlight" <jmsstarlight.gmail.com>
> >> wrote:
> >>
> >> > I think I have no more problems with the gb radii which I've found it
> in
> >> > the manual :) but the question with the
> >> >
> >> > 0) cut-offs is still exist because in case of in vacuum simulation I
> use
> >> > infitinive cutoffs but not sure what should I do in case of gb.
> >> >
> >> > Some additional question:
> >> > 1) Does the simulation with gb support NPT besides NVT (I guess that
> >> with
> >> > the infinitive cutoffs it could be quite impossiblebut who knows:) )
> >> >
> >> > 2) I need to add restraints which will prohibit isomerisation of
> peptide
> >> > bond (it's needed in case of amd or sa simulations) in loops. In this
> >> > simulation I've already frize all atoms of not-loops by means of
> >> addition
> >> >
> >> > restraint_wt=10.0, restraintmask=':6-33,40-68,76-
> >> > 109,120-143,177-204,216-246,256-286',
> >> >
> >> > so what should be provided besides to prevent rotation around omega
> >> > dihedral angle?
> >> >
> >> >
> >> > 3) Is there some additional options to GB for membrane protein
> >> simulation
> >> > w/o application of restrains to membrane-embedded part (assuming that
> >> some
> >> > part of protein should be in fact in water with di-electric 80 and
> >> another
> >> > in membrane with di-electirc= 2 )? How it could be taken into the
> >> account
> >> > in the GB simulation?
> >> >
> >> > TFH to everyone,
> >> >
> >> > James
> >> >
> >> >
> >> > 2014-07-17 11:27 GMT+04:00 James Starlight <jmsstarlight.gmail.com>:
> >> >
> >> > > Thanks for suggestion!
> >> > >
> >> > > Do you think that gb 8 model (in comparison to other gb models)
> might
> >> be
> >> > > best solution for membrane protein with frozen *membrane embedded*
> >> > elements
> >> > > of its secondary structure? Some technical questions:
> >> > > 1)should I use infinitive cutoffs (999) during IS simulation ?
> >> > > 2) I'm not sure If I assigned gb radii correctly - does it should be
> >> done
> >> > > explicitly during processing of my model by tleap ? Are there
> special
> >> > > values for the membrane proteins might be?
> >> > >
> >> > >
> >> > > TFH,
> >> > >
> >> > >
> >> > > James
> >> > >
> >> > >
> >> > > 2014-07-16 17:37 GMT+02:00 Carlos Simmerling <
> >> > carlos.simmerling.gmail.com>
> >> > > :
> >> > >
> >> > > I think that if you choose a reasonably accurate GB model then this
> >> task
> >> > is
> >> > >> much easier than with explicit water. Explicit may be more
> accurate,
> >> but
> >> > >> sampling loop conformational changes can be too slow. You always
> >> have to
> >> > >> trade off accuracy and sampling. I would suggest giving our igb=8
> >> model
> >> > a
> >> > >> try (read the manual for suggestions on radii, etc). As always,
> >> you'll
> >> > >> want
> >> > >> to make sure you have some data against which you can validate any
> >> > >> predictions that you make about structure. Regarding the REMD part,
> >> it's
> >> > >> another good reason to give GB a try. REMD in explicit water is
> >> > expensive
> >> > >> (many replicas) and quite slow. Freezing part could be a problem-
> I'm
> >> > not
> >> > >> sure if you can do that in all of the Amber MD codes (using the GB
> >> pmemd
> >> > >> code is probably best). You could choose positional restraints on
> the
> >> > >> non-loop region to keep it fixed. Having it be totaly frozen might
> >> not
> >> > be
> >> > >> good anyway, since there may be some adjustment needed for
> different
> >> > loop
> >> > >> options.
> >> > >>
> >> > >> Another possibility is to use loop modeling that doesn't involve
> MD -
> >> > such
> >> > >> as the analytical approaches. Then you might rescore the various
> >> models
> >> > >> with a good MM+GBSA approach.
> >> > >> good luck
> >> > >> CS
> >> > >>
> >> > >>
> >> > >> On Thu, Jul 10, 2014 at 5:44 AM, James Starlight <
> >> > jmsstarlight.gmail.com>
> >> > >> wrote:
> >> > >>
> >> > >> > some suggestions.
> >> > >> >
> >> > >> > some people gave me evidence that for my task (see a full set of
> >> loop
> >> > >> > confirmations and chose most probable) it will not good to use
> >> > implicit
> >> > >> > solvent +amd because this will produce very unphysical
> >> thermodynamics
> >> > >> isn't
> >> > >> > it?
> >> > >> >
> >> > >> > In fact I'm dealing with the membrane protein where
> >> membrane-embeded
> >> > >> part
> >> > >> > should be fixed (I would not refine something here) and loops
> which
> >> > are
> >> > >> > exposed to the solvent must be free to move. In this regards I've
> >> > tried
> >> > >> to
> >> > >> > applied gb model of IS with the frozen of not refined part of my
> >> > >> protein.
> >> > >> > Will it be reasonable to use REMD with such implicit solvent
> model
> >> for
> >> > >> the
> >> > >> > refinement? How It could be possible to really simplify REMD
> >> protocol
> >> > >> for
> >> > >> > such loop prediction (e,g using small number of replicas or not).
> >> > >> > Some another suggestion (e.g brut force md with gb models)?
> >> > >> >
> >> > >> > James
> >> > >> >
> >> > >> >
> >> > >> >
> >> > >> > 2014-07-09 12:01 GMT+02:00 James Starlight <
> jmsstarlight.gmail.com
> >> >:
> >> > >> >
> >> > >> > > some updating of my issue
> >> > >> > >
> >> > >> > > I need to refine regions of my model consisted of water exposed
> >> > 10-15
> >> > >> > > residues loops in which I'm not certain after its homology
> >> modeling.
> >> > >> For
> >> > >> > > this task I'd like to
> >> > >> > > 1) Freeze all atoms of the protein consisted of the secondary
> >> > >> structure
> >> > >> > > elements in which I'm not interest.
> >> > >> > > 2)Use some implicit solvent model for this simulation.
> >> > >> > > 3) Use some enhancing sampling technique to sample all possible
> >> > >> > > conformation of the loops at short timescale but keeping
> initial
> >> > >> > > thermodynamics of the system => predict possible folding in the
> >> > loops
> >> > >> > > during the refinement.
> >> > >> > >
> >> > >> > > please suggest me possible GB implicit solvent model as well as
> >> > >> enhanced
> >> > >> > > sampling engine (I'm chosing between replica exchange and
> >> > accelerated
> >> > >> md
> >> > >> > > with dihedral boost only). Any additional methods?
> >> > >> > >
> >> > >> > > I'll be very thankful to all,
> >> > >> > >
> >> > >> > >
> >> > >> > > James
> >> > >> > >
> >> > >> > >
> >> > >> > > 2014-06-14 22:21 GMT+02:00 James Starlight <
> >> jmsstarlight.gmail.com
> >> > >:
> >> > >> > >
> >> > >> > > Also I'll be thankful if someone check my example SA script
> with
> >> > >> applied
> >> > >> > >> multiple position restraints to some segment of my protein
> (here
> >> > I'd
> >> > >> > like
> >> > >> > >> to freeze all atoms but not loop which I'd like to sample).
> >> > >> > >>
> >> > >> > >> SA with posres
> >> > >> > >> &cntrl
> >> > >> > >> imin=0,
> >> > >> > >> ntx=1,
> >> > >> > >> irest=0,
> >> > >> > >> ntc=2,
> >> > >> > >> ntf=2,
> >> > >> > >> tol=0.0000001,
> >> > >> > >> nstlim=50000,
> >> > >> > >> ntt=3,
> >> > >> > >> gamma_ln=1.0,
> >> > >> > >> ntr=1,
> >> > >> > >> ig=-1,
> >> > >> > >> ntpr=100,
> >> > >> > >> ntwr=10000,
> >> > >> > >> ntwx=100,
> >> > >> > >> dt=0.002,
> >> > >> > >> nmropt=1,
> >> > >> > >> ntb=0,
> >> > >> > >> ntp=0,
> >> > >> > >> cut=999.0,
> >> > >> > >> ioutfm=1,
> >> > >> > >> ntxo=2,
> >> > >> > >> igb=1,
> >> > >> > >> /
> >> > >> > >> &wt
> >> > >> > >> type='TEMP0',
> >> > >> > >> istep1=0,
> >> > >> > >> istep2=10000,
> >> > >> > >> value1=0.0,
> >> > >> > >> value2=103.0 /
> >> > >> > >> &wt
> >> > >> > >> type='TEMP0',
> >> > >> > >> istep1=10001,
> >> > >> > >> istep2=20000,
> >> > >> > >> value1=103.0,
> >> > >> > >> value2=203.0 /
> >> > >> > >> &wt
> >> > >> > >> type='TEMP0',
> >> > >> > >> istep1=20001,
> >> > >> > >> istep2=50000,
> >> > >> > >> value1=203.0,
> >> > >> > >> value2=303.0 /
> >> > >> > >> &wt type='END' /
> >> > >> > >> fixed
> >> > >> > >> 1000.0
> >> > >> > >> RES 1 67
> >> > >> > >> END
> >> > >> > >> fixed
> >> > >> > >> 1000.0
> >> > >> > >> RES 75 142
> >> > >> > >> END
> >> > >> > >> fixed
> >> > >> > >> 1000.0
> >> > >> > >> RES 169 241
> >> > >> > >> END
> >> > >> > >> fixed
> >> > >> > >> 1000.0
> >> > >> > >> RES 249 286
> >> > >> > >> END
> >> > >> > >> END
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> Here I try to heat my system in 3 subsequent steps performing
> >> > >> simulation
> >> > >> > >> using implicit solvent without PBC. Does it correct in
> general?
> >> I
> >> > >> could
> >> > >> > not
> >> > >> > >> visualize my system in VMD using
> >> > >> > >> vmd -parm7 b2ar_Amber.prmtop -netcdf sa.nc
> >> > >> > >> what should I fix here?
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> James
> >> > >> > >>
> >> > >> > >>
> >> > >> > >> 2014-06-13 23:50 GMT+04:00 James Starlight <
> >> jmsstarlight.gmail.com
> >> > >:
> >> > >> > >>
> >> > >> > >> Dear Vlad,
> >> > >> > >>>
> >> > >> > >>>
> >> > >> > >>> many thanks for suggestions. I've already seen some papers
> >> > >> describing
> >> > >> > >>> some methodologies of structural refinement based of some
> >> enhanced
> >> > >> > sampling
> >> > >> > >>> methods. However in case of loop refinement what could be
> >> expected
> >> > >> > from the
> >> > >> > >>> brute-force md with aplied restraints on the rest of the
> >> protein
> >> > >> > (excluding
> >> > >> > >>> refined loops) using 1) implicit solvent 2) some
> >> > >> > high-temperatutre-based
> >> > >> > >>> method like simulating annealing.
> >> > >> > >>>
> >> > >> > >>> James
> >> > >> > >>>
> >> > >> > >>>
> >> > >> > >>> 2014-05-28 11:53 GMT+04:00 Vlad Cojocaru <
> >> > >> > >>> vlad.cojocaru.mpi-muenster.mpg.de>:
> >> > >> > >>>
> >> > >> > >>> Dear James,
> >> > >> > >>>>
> >> > >> > >>>> I am afraid you'd have to do some reading ... Its very hard
> to
> >> > >> believe
> >> > >> > >>>> that somebody on this list has the time to give you detailed
> >> > >> > >>>> instructions. What you ask for is a summary of many
> different
> >> > >> papers.
> >> > >> > >>>> The Amber manual has an example of simulated annealing
> >> protocol
> >> > for
> >> > >> > NMR
> >> > >> > >>>> refinement which used to be with distance dependent
> dielectric
> >> > >> (maybe
> >> > >> > it
> >> > >> > >>>> has changed in the meantime). Anyhow, you'd have to adapt
> >> that to
> >> > >> the
> >> > >> > >>>> implicit solvent model you wish to use. The implicit solvent
> >> > models
> >> > >> > are
> >> > >> > >>>> all well documented in the corresponding publications which
> >> are
> >> > >> > >>>> referenced in the Amber manual.
> >> > >> > >>>>
> >> > >> > >>>> Besides, take care how you interpret your results. The
> longer
> >> the
> >> > >> > loops,
> >> > >> > >>>> the less you can rely on the loop refinement. You'd need to
> >> run a
> >> > >> > number
> >> > >> > >>>> of different simulations, maybe even test different force
> >> fields
> >> > >> ...
> >> > >> > >>>> Especially if loops are functionally important, you may
> easily
> >> > draw
> >> > >> > >>>> wrong conclusions from such refinements. Comparison with
> >> > >> experiments
> >> > >> > is
> >> > >> > >>>> always good.
> >> > >> > >>>>
> >> > >> > >>>> Best,
> >> > >> > >>>> Vlad
> >> > >> > >>>>
> >> > >> > >>>>
> >> > >> > >>>> On 05/28/2014 09:29 AM, James Starlight wrote:
> >> > >> > >>>> > I try to specify my question.
> >> > >> > >>>> >
> >> > >> > >>>> > I suppose that force field based simulated annealing with
> >> > >> positions
> >> > >> > >>>> > restraints applied to the all protein atoms but not for
> >> loops
> >> > >> which
> >> > >> > >>>> I'd
> >> > >> > >>>> > like to refine might be exactly what I'm looking for.
> Could
> >> > >> someone
> >> > >> > >>>> suggest
> >> > >> > >>>> > appropriate SA setups for such loop refirement: e.g I'm
> >> > >> interesting
> >> > >> > in
> >> > >> > >>>> > number of SA windows, coupling constants in each windows,
> >> > >> > appropriate
> >> > >> > >>>> > implicit solvent models?
> >> > >> > >>>> >
> >> > >> > >>>> >
> >> > >> > >>>> > James
> >> > >> > >>>> >
> >> > >> > >>>> >
> >> > >> > >>>> > 2014-05-26 14:06 GMT+04:00 James Starlight <
> >> > >> jmsstarlight.gmail.com
> >> > >> > >:
> >> > >> > >>>> >
> >> > >> > >>>> >> Dear Amber's users!
> >> > >> > >>>> >>
> >> > >> > >>>> >>
> >> > >> > >>>> >> I need to refine some flexible regions (mainly long loop
> >> and
> >> > >> linker
> >> > >> > >>>> >> regions) of my proteins prior to the production MD run
> >> using
> >> > >> some
> >> > >> > >>>> enhanced
> >> > >> > >>>> >> sampling engines implemented in Amber like accelerated
> >> > molecular
> >> > >> > >>>> dynamics
> >> > >> > >>>> >> or simulated annealing. Please provide me with some
> basic
> >> > >> ideas of
> >> > >> > >>>> the
> >> > >> > >>>> >> easiliest realization of these methods in amber including
> >> > >> suitable
> >> > >> > >>>> implicit
> >> > >> > >>>> >> solvent models for such task with the tutorials and
> further
> >> > >> > reading.
> >> > >> > >>>> >>
> >> > >> > >>>> >>
> >> > >> > >>>> >> TFH,
> >> > >> > >>>> >>
> >> > >> > >>>> >> James
> >> > >> > >>>> >>
> >> > >> > >>>> > _______________________________________________
> >> > >> > >>>> > AMBER mailing list
> >> > >> > >>>> > AMBER.ambermd.org
> >> > >> > >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >> > >>>> >
> >> > >> > >>>>
> >> > >> > >>>> --
> >> > >> > >>>> Dr. Vlad Cojocaru
> >> > >> > >>>> Max Planck Institute for Molecular Biomedicine
> >> > >> > >>>> Department of Cell and Developmental Biology
> >> > >> > >>>> Röntgenstrasse 20, 48149 Münster, Germany
> >> > >> > >>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >> > >> > >>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >> > >> > >>>>
> >> > >> > >>>>
> >> > >> > >>>> _______________________________________________
> >> > >> > >>>> AMBER mailing list
> >> > >> > >>>> AMBER.ambermd.org
> >> > >> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >> > >> > >>>>
> >> > >> > >>>
> >> > >> > >>>
> >> > >> > >>
> >> > >> > >
> >> > >> > _______________________________________________
> >> > >> > AMBER mailing list
> >> > >> > AMBER.ambermd.org
> >> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >> >
> >> > >> _______________________________________________
> >> > >> AMBER mailing list
> >> > >> AMBER.ambermd.org
> >> > >> http://lists.ambermd.org/mailman/listinfo/amber
> >> > >>
> >> > >
> >> > >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> _______________________________________________
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Received on Thu Jul 17 2014 - 10:30:04 PDT
