[gmx-users] Fwd: Selecting the temperature distribution

Tue Apr 23 15:06:47 CEST 2013

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
> Mobile no. - 010-5818-3680
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