Re: [gmx-users] Fwd: Selecting the temperature distribution
Likewise, I agreed with what Massimo said. As an example, I recently did a fairly large set of REMD simulations of a 320-atom disordered peptide with rather more water and many fewer replicas than you propose. I did so because I expected low barriers and large maximum diameter (the latter from an implicit-solvent REMD). Even after the fact, I cannot demonstrate that my decisions were correct (and probably could not even if I could have produced clearly converged ensembles). Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
This hints at an interesting protocol/attempt, at least for a sort of newbie like me. Can you elaborate? Did they exchange? On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote: Likewise, I agreed with what Massimo said. As an example, I recently did a fairly large set of REMD simulations of a 320-atom disordered peptide with rather more water and many fewer replicas than you propose. I did so because I expected low barriers and large maximum diameter (the latter from an implicit-solvent REMD). Even after the fact, I cannot demonstrate that my decisions were correct (and probably could not even if I could have produced clearly converged ensembles). Mark -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
Yes, I got exchanges. By construction! :-) Email me off-list if you would like a methods description (for what it is worth). Mark On Thu, Apr 25, 2013 at 1:11 PM, massimo sandal deviceran...@gmail.comwrote: This hints at an interesting protocol/attempt, at least for a sort of newbie like me. Can you elaborate? Did they exchange? On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote: Likewise, I agreed with what Massimo said. As an example, I recently did a fairly large set of REMD simulations of a 320-atom disordered peptide with rather more water and many fewer replicas than you propose. I did so because I expected low barriers and large maximum diameter (the latter from an implicit-solvent REMD). Even after the fact, I cannot demonstrate that my decisions were correct (and probably could not even if I could have produced clearly converged ensembles). Mark -- gmx-users mailing listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
On 4/23/13 9:43 PM, bharat gupta wrote: 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 ?? I haven't said anything because I agree with what Massimo has already told you. If that is comforting in some way to know, then so be it, but I think it is rather rude to suggest that you would rather someone else answer your question, even after being given thorough and correct insight. This is a community forum with many experts who have valuable insight to share. -Justin On Tue, Apr 23, 2013 at 11:15 PM, massimo sandal deviceran...@gmail.comwrote: 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
Re: [gmx-users] Fwd: Selecting the temperature distribution
2013/4/24 Justin Lemkul jalem...@vt.edu I haven't said anything because I agree with what Massimo has already told you. If that is comforting in some way to know, then so be it, but I think it is rather rude to suggest that you would rather someone else answer your question, even after being given thorough and correct insight. This is a community forum with many experts who have valuable insight to share. Well, he couldn't know that my insight was right (honestly, I was expecting to be corrected!). I think he did right by trying to be double-sure, I don't feel offended by it :) -- gmx-users mailing listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
I think it should be me who should be sorry. I should have asked the question again in the forum without referring to some particular individual. On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal deviceran...@gmail.comwrote: 2013/4/24 Justin Lemkul jalem...@vt.edu I haven't said anything because I agree with what Massimo has already told you. If that is comforting in some way to know, then so be it, but I think it is rather rude to suggest that you would rather someone else answer your question, even after being given thorough and correct insight. This is a community forum with many experts who have valuable insight to share. Well, he couldn't know that my insight was right (honestly, I was expecting to be corrected!). I think he did right by trying to be double-sure, I don't feel offended by it :) -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
Don't be sorry. It's okay. It's just cultural differences. 2013/4/24 bharat gupta bharat.85.m...@gmail.com I think it should be me who should be sorry. I should have asked the question again in the forum without referring to some particular individual. On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal deviceran...@gmail.com wrote: 2013/4/24 Justin Lemkul jalem...@vt.edu I haven't said anything because I agree with what Massimo has already told you. If that is comforting in some way to know, then so be it, but I think it is rather rude to suggest that you would rather someone else answer your question, even after being given thorough and correct insight. This is a community forum with many experts who have valuable insight to share. Well, he couldn't know that my insight was right (honestly, I was expecting to be corrected!). I think he did right by trying to be double-sure, I don't feel offended by it :) -- gmx-users mailing listgmx-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 listgmx-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 listgmx-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] Fwd: Selecting the temperature distribution
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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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 listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] Fwd: Selecting the temperature distribution
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 listgmx-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 listgmx-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 listgmx-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 listgmx-users@gromacs.org
Re: [gmx-users] Fwd: Selecting the temperature distribution
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] Fwd: Selecting the temperature distribution
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 listgmx-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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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.comwrote: 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 listgmx-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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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/
Re: [gmx-users] Fwd: Selecting the temperature distribution
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
Re: [gmx-users] Fwd: Selecting the temperature distribution
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.comwrote: 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,
Re: [gmx-users] Fwd: Selecting the temperature distribution
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,
Re: [gmx-users] Fwd: Selecting the temperature distribution
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.comwrote: 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 :
