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.m...@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 <deviceran...@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.m...@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 < > deviceran...@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.m...@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 < > > > deviceran...@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.m...@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 < > > > > > deviceran...@gmail.com > > > > > > > >wrote: > > > > > > > > > > > > > > > Look here: http://folding.bmc.uu.se/remd/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 2013/4/23 bharat gupta <bharat.85.m...@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 > > > > > > > > > -- > > > > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > > > > * Please search the archive at > > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > > > > > posting! > > > > > > > > > * Please don't post (un)subscribe requests to the list. Use > > the > > > > > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > > > > > * Can't post? 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Read > > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > -- > > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > > * Please search the archive at > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > > > posting! > > > > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > -- > > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > > * Please search the archive at > > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > > posting! > > > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Bharat > > > > > Ph.D. Candidate > > > > > Biomolecular Engineering Laboratory > > > > > Pusan National University > > > > > South Korea > > > > > Mobile no. - 010-5818-3680 > > > > > -- > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > > > > > * Please don't post (un)subscribe requests to the list. Use the > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > > * Can't post? 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