[gmx-users] Fwd: Selecting the temperature distribution

Wed Apr 24 03:43:39 CEST 2013

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 <devicerandom at 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.monu at 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 <devicerandom at 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.monu at 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 <
> > devicerandom at 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.monu at 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 <
> > > > devicerandom at 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.monu at 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 <
> > > > > > devicerandom at 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.monu at 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 <
> > > > > > > > devicerandom at gmail.com
> > > > > > > > > > >wrote:
> > > > > > > > > >
> > > > > > > > > > > Look here: http://folding.bmc.uu.se/remd/
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > 2013/4/23 bharat gupta <bharat.85.monu at 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
> > > > > > > > > > > > --
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> > > > > > > > --
> > > > > > > > Bharat
> > > > > > > > Ph.D. Candidate
> > > > > > > > Biomolecular Engineering Laboratory
> > > > > > > > Pusan National University
> > > > > > > > South Korea
> > > > > > > > Mobile no. - 010-5818-3680
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> > > > > > Bharat
> > > > > > Ph.D. Candidate
> > > > > > Biomolecular Engineering Laboratory
> > > > > > Pusan National University
> > > > > > South Korea
> > > > > > Mobile no. - 010-5818-3680
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-- 
Bharat
Ph.D. Candidate
Biomolecular Engineering Laboratory
Pusan National University
South Korea
Mobile no. - 010-5818-3680