[gmx-users] Fwd: Selecting the temperature distribution

massimo sandal devicerandom at gmail.com
Tue Apr 23 16:15:35 CEST 2013 

In general, the smaller is your system, the less temperatures you will need
(and you'll have better performance).

Notice however that implicit solvent, while surely a possibility worth
considering, is not usually considered to be very good -take care that if
you write a paper from implicit solvent results, reviewers might not be
happy. There is a chance that the results coming out of your simulation
might be nonsense. Discuss this choice with your supervisor and/or with
expert colleagues who know about limitations of implicit solvent. You need
to be able to justify your choice scientifically -for example testing it
with a known,similar system and observing that implicit solvent reproduces
the behaviour of that system in explicit solvent well.

About reducing the box size, by all means try it, but always make sure it
is large enough to avoid that the periodic copies of your molecule see each
other. See
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand
be sure to understand it.


2013/4/23 bharat gupta <bharat.85.monu at gmail.com>

> Thanks a lot for your prompt responses. By using implicit solvent , I am
> getting on 9 temperature values. I think this should work , I will try it
> out. Also, i checked that when the no. of water molecules are reduced , the
> no. of temp. values are also reduced. If I reduce the no. of water
> molecules or reduce the size of box , will it help. As of now I am using
> octahedron box.
>
>
> On Tue, Apr 23, 2013 at 10:43 PM, massimo sandal <devicerandom at gmail.com
> >wrote:
>
> > It depends on what you want to do. Possible it is certainly possible, but
> > you can't be guaranteed to observe the conformational changes you desire
> to
> > observe. Again, it does not depend only on the REMD, but also on the
> length
> > of it. How long will it be? 10 ns? 100? 1000? 10.000? Plus, it also
> depends
> > on your system itself -and this you cannot know without trying.
> >
> > If you want to improve sampling beyond what standard REMD can do, to
> > exploit your computational resources at the best, you can look into other
> > approaches like solute tempering (
> > http://www.pnas.org/content/102/39/13749.abstract ), or metadynamics (
> > http://en.wikipedia.org/wiki/Metadynamics ). However I advise you to
> study
> > *well* this kind of things, talk with experts in these techniques,  and
> > remember that there is no guarantee any of them will bring the result you
> > want. Good luck! :)
> >
> >
> >
> >
> > 2013/4/23 bharat gupta <bharat.85.monu at gmail.com>
> >
> > > So, my final question is whether is possible to do REMD for my system,
> > > using the computational resource that I have.
> > >
> > >
> > > On Tue, Apr 23, 2013 at 10:06 PM, massimo sandal <
> devicerandom at gmail.com
> > > >wrote:
> > >
> > > > Who knows? It depends on the size of your peptide, on the energy
> > > landscape,
> > > > on how long is the run you plan to do. I would bet on "no", however.
> > > >
> > > >
> > > > 2013/4/23 bharat gupta <bharat.85.monu at gmail.com>
> > > >
> > > > > But if I choose a smaller temperature range , would it be possible
> to
> > > > > observe any folding event ??
> > > > >
> > > > >
> > > > > On Tue, Apr 23, 2013 at 9:16 PM, massimo sandal <
> > > devicerandom at gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Thanks, now it's clearer.
> > > > > >
> > > > > > > Now, how can I temp. from these, so that the replicas can
> > exchange
> > > > ...
> > > > > >
> > > > > > You can't, I would say. The system you have requires so many
> > replicas
> > > > to
> > > > > > exchange properly from the two temperature extremes you set up.
> As
> > > you
> > > > > have
> > > > > > seen, if you pick up temperatures in that range randomly, they
> > can't
> > > > > > exchange anymore. They are too far away.
> > > > > >
> > > > > > I would choose a smaller temperature range. There is little else
> > you
> > > > can
> > > > > > do, I think.
> > > > > >
> > > > > >
> > > > > > 2013/4/23 bharat gupta <bharat.85.monu at gmail.com>
> > > > > >
> > > > > > > Sorry for that, I explain it again. Actually, I used the this
> > link
> > > to
> > > > > > > generate a temp. distribution. But I can do REMD for 56
> replicas
> > > > only,
> > > > > > as I
> > > > > > > have 56 processors available. The t-remd calculator provides
> 220
> > > > > > > temperature values :
> > > > > > >
> > > > > > > 300.00, 301.01, 302.02, 303.04, 304.06, 305.08, 306.11, 307.14,
> > > > 308.17,
> > > > > > > 309.20, 310.24, 311.27, 312.32, 313.36, 314.40, 315.45, 316.50,
> > > > 317.56,
> > > > > > > 318.61, 319.68, 320.74, 321.81, 322.88, 323.95, 325.02, 326.10,
> > > > 327.18,
> > > > > > > 328.26, 329.35, 330.44, 331.53, 332.63, 333.72, 334.83, 335.93,
> > > > 337.04,
> > > > > > > 338.15, 339.26, 340.37, 341.49, 342.61, 343.74, 344.87, 346.00,
> > > > 347.13,
> > > > > > > 348.27, 349.41, 350.55, 351.69, 352.85, 354.00, 355.15, 356.31,
> > > > 357.47,
> > > > > > > 358.63, 359.80, 360.97, 362.14, 363.32, 364.49, 365.68, 366.86,
> > > > 368.05,
> > > > > > > 369.24, 370.44, 371.64, 372.84, 374.05, 375.26, 376.47, 377.68,
> > > > 378.90,
> > > > > > > 380.12, 381.34, 382.57, 383.80, 385.03, 386.27, 387.51, 388.75,
> > > > 390.00,
> > > > > > > 391.25, 392.51, 393.76, 395.02, 396.29, 397.56, 398.83, 400.10,
> > > > 401.38,
> > > > > > > 402.68, 403.96, 405.25, 406.54, 407.84, 409.14, 410.44, 411.74,
> > > > 413.05,
> > > > > > > 414.40, 415.71, 417.03, 418.36, 419.68, 421.01, 422.35, 423.68,
> > > > 425.03,
> > > > > > > 426.37, 427.72, 429.07, 430.43, 431.79, 433.15, 434.52, 435.89,
> > > > 437.26,
> > > > > > > 438.64, 440.02, 441.40, 442.79, 444.18, 445.58, 446.98, 448.38,
> > > > 449.79,
> > > > > > > 451.20, 452.62, 454.03, 455.46, 456.88, 458.31, 459.75, 461.18,
> > > > 462.63,
> > > > > > > 464.08, 465.53, 466.99, 468.45, 469.91, 471.38, 472.85, 474.32,
> > > > 475.80,
> > > > > > > 477.28, 478.76, 480.25, 481.74, 483.24, 484.74, 486.25, 487.76,
> > > > 489.27,
> > > > > > > 490.79, 492.31, 493.83, 495.36, 496.90, 498.43, 499.97, 501.52,
> > > > 503.07,
> > > > > > > 504.63, 506.18, 507.78, 509.34, 510.91, 512.49, 514.07, 515.65,
> > > > 517.24,
> > > > > > > 518.83, 520.43, 522.03, 523.64, 525.25, 526.86, 528.48, 530.10,
> > > > 531.73,
> > > > > > > 533.36, 535.00, 536.63, 538.27, 539.92, 541.58, 543.23, 544.90,
> > > > 546.56,
> > > > > > > 548.23, 549.90, 551.58, 553.27, 554.96, 556.65, 558.35, 560.06,
> > > > 561.76,
> > > > > > > 563.48, 565.19, 566.92, 568.65, 570.38, 572.11, 573.85, 575.60,
> > > > 577.47,
> > > > > > > 579.23, 580.99, 582.76, 584.52, 586.30, 588.08, 589.86, 591.65,
> > > > 593.44,
> > > > > > > 595.24, 597.04, 598.85, 600.66
> > > > > > >
> > > > > > >
> > > > > > > Now, how can I temp. from these, so that the replicas can
> > exchange
> > > > ...
> > > > > > >
> > > > > > >
> > > > > > > On Tue, Apr 23, 2013 at 9:04 PM, massimo sandal <
> > > > > devicerandom at gmail.com
> > > > > > > >wrote:
> > > > > > >
> > > > > > > > I don't understand your question. If you got the temperature
> > > > > > > distribution,
> > > > > > > > what else do you need?
> > > > > > > >
> > > > > > > >
> > > > > > > > 2013/4/23 bharat gupta <bharat.85.monu at gmail.com>
> > > > > > > >
> > > > > > > > > I have got the temperature distribution from the same link,
> > but
> > > > how
> > > > > > to
> > > > > > > > > select evenly spaced temperatures for 56 replicas, I need
> to
> > > know
> > > > > > that
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Tue, Apr 23, 2013 at 6:21 PM, massimo sandal <
> > > > > > > devicerandom at gmail.com
> > > > > > > > > >wrote:
> > > > > > > > >
> > > > > > > > > > Look here: http://folding.bmc.uu.se/remd/
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > 2013/4/23 bharat gupta <bharat.85.monu at gmail.com>
> > > > > > > > > >
> > > > > > > > > > > Dear gmx users,
> > > > > > > > > > >
> > > > > > > > > > > I am planning to run REMD for a peptide (406 atoms )+
> > > solvent
> > > > > > > system
> > > > > > > > > > > (27639). The temperature range I selected is from 300
> to
> > > > 500. I
> > > > > > > want
> > > > > > > > to
> > > > > > > > > > > select appropriate temp. for 56 replicas. I randomly
> > chose
> > > > some
> > > > > > > temp
> > > > > > > > > > > distribution and the exchange probabilities was 0.0. I
> > know
> > > > > that
> > > > > > we
> > > > > > > > can
> > > > > > > > > > use
> > > > > > > > > > > the formula  Ti=T0*ek*i, but what is the value for i
> and
> > K
> > > > here
> > > > > > ??
> > > > > > > > > > >
> > > > > > > > > > > --------
> > > > > > > > > > > BHARAT
> > > > > > > > > > > --
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> > > > > > > --
> > > > > > > Bharat
> > > > > > > Ph.D. Candidate
> > > > > > > Biomolecular Engineering Laboratory
> > > > > > > Pusan National University
> > > > > > > South Korea
> > > > > > > Mobile no. - 010-5818-3680
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