Dear Justin/Mark, I have asked this question previously in the forum, I got some reply from other members. It will be more useful if you can provide you expert comments on the same. 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 (as I have 56 processors available). I used the t-remd calculator for temp. generation. It provided some 200 temp. values. Here are my questions : 1. Is it possible to select equally spaced temp. values from those values ?? 2. I checked that reducing the no. of water mol. decreases the temp. values. What if I reduce the no. of water mol., will if affect the simulation ??
On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal <deviceran...@gmail.com>wrote: > In general, the smaller is your system, the less temperatures you will need > (and you'll have better performance). > > Notice however that implicit solvent, while surely a possibility worth > considering, is not usually considered to be very good -take care that if > you write a paper from implicit solvent results, reviewers might not be > happy. There is a chance that the results coming out of your simulation > might be nonsense. Discuss this choice with your supervisor and/or with > expert colleagues who know about limitations of implicit solvent. You need > to be able to justify your choice scientifically -for example testing it > with a known,similar system and observing that implicit solvent reproduces > the behaviour of that system in explicit solvent well. > > About reducing the box size, by all means try it, but always make sure it > is large enough to avoid that the periodic copies of your molecule see each > other. See > > http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water#Box_Preparationand > be sure to understand it. > > > 2013/4/23 bharat gupta <bharat.85.m...@gmail.com> > > > 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 <deviceran...@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.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? 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