[gmx-users] Fwd: Selecting the temperature distribution
bharat gupta
bharat.85.monu at gmail.com
Tue Apr 23 15:55:47 CEST 2013
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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> > > > Ph.D. Candidate
> > > > Biomolecular Engineering Laboratory
> > > > Pusan National University
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