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? 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
