In general, look in the literature what other people have done on similar systems, and try to go from there.
2013/4/23 massimo sandal <deviceran...@gmail.com> > 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/Searchbefore >> > > > > 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 >> > > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > > > -- >> > > > > > > -- >> > > > > > > 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? 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? 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 >> > > -- 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