[gmx-users] Fwd: Selecting the temperature distribution

Tue Apr 23 15:43:45 CEST 2013

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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> > > --
> > > Bharat
> > > Ph.D. Candidate
> > > Biomolecular Engineering Laboratory
> > > Pusan National University
> > > South Korea
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