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
>> >
>> _______________________________________________
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Received on Thu Jul 17 2014 - 10:00:02 PDT
