[gmx-users] Fwd: Selecting the temperature distribution

Tue Apr 23 14:16:28 CEST 2013

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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