AMBER Archive (2006)

Subject: Re: AMBER: problem of the REMD with nmr constraints

From: wenfei Li (wfli_at_biophy.nju.edu.cn)
Date: Sat Nov 25 2006 - 19:56:05 CST

Dear Prof. Simmerling,

Thank you very much for your prompt reply. I'll try amber9 for this problem and tell you the result.

Wenfei Li

> can you try amber9 to see if this problem still happens?
>

> wenfei Li wrote:
>
> >Dear AMBER users,
> >
> > I'm performing a replica-exchange MD simulation for a zinc ion containing protein system using AMBER8. The zinc ion is not bonded to any residue.
> >
> > When I add the nmr constraint (distance constraint) between the zinc ion and the protein atoms by setting nmropt=1, the exchange behavior is abnormal: the temperatures of each replicas can only be switched to their very near neighbors and then come back to their original values quickly. But, when without the nmr constraint, the exchange behavior is normal: the temperatures of each replicas can variate within a wide temperature range randomly.
> >
> >Is this a bug or something wrong with my input parameters?
> >
> >Here is one of my input files of the remd simulation with nmropt=1.
> >
> >title ----title ----
> > &cntrl
> > imin = 0, nstlim = 400, dt = 0.002,
> > igb = 2, gbsa = 1, saltcon = 0.2,
> > ntx = 5, temp0 = 282.86, tautp = 0.1,
> > ntt = 1, irest = 1, nmropt = 1,
> > ntc = 2, ntf = 2, ntb = 0,
> > ntwx = 200,ntwr = 400, ntpr = 200,
> > scee = 1.2, cut = 30.0,
> > ntr = 0, numexchg = 250000,
> > nscm = 300,
> > /
> > &wt type='REST', istep1=0,istep2=400,value1=1.0,
> > value2=1.0, /
> >
> > &wt type='END' /
> >LISTOUT=POUT
> >DISANG=RST.wc
> >
> >
> >And the distance constraints file RST.wc is:
> >
> >#
> ># 41 Zn Zn 6 HIE ND1 2.01 2.21
> > &rst
> > ixpk= 0, nxpk= 0, iat= 599, 92, r1= 1.51, r2= 2.01, r3= 2.21, r4= 2.71,
> > rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> > &end
> >#
> ># 41 Zn Zn 13 HID NE2 2.05 2.25
> > &rst
> > ixpk= 0, nxpk= 0, iat= 599, 195, r1= 1.55, r2= 2.05, r3= 2.25, r4= 2.75, &end
> >#
> ># 41 Zn Zn 14 HIE ND1 2.19 2.39
> > &rst
> > ixpk= 0, nxpk= 0, iat= 599, 208, r1= 1.69, r2= 2.19, r3= 2.39, r4= 2.89, &end
> >#
> ># 41 Zn Zn 11 GLU OE1 2.01 2.21
> > &rst
> > ixpk= 0, nxpk= 0, iat= 599, 163, r1= 1.51, r2= 2.01, r3= 2.21, r4= 2.71, &end
> >#
> ># 41 Zn Zn 11 GLU OE2 2.02 2.21
> > &rst
> > ixpk= 0, nxpk= 0, iat= 599, 164, r1= 1.52, r2= 2.02, r3= 2.21, r4= 2.71, &end
> >
> >
> >
> >Below is the remlog file with nmropt=1 at 800th exchange step. The temperature distribution does not change very much from the initial one.
> >
> > # exchange 800
> > 1 -1.00 273.63 -1142.35 282.86 282.86
> > 2 1.01 286.94 -1165.77 290.95 299.31
> > 3 0.99 302.13 -1149.84 299.31 290.95
> > 4 -1.00 312.31 -1136.91 307.97 307.97
> > 5 -1.00 329.02 -1110.67 316.90 316.90
> > 6 -1.00 329.00 -1129.73 326.15 326.15
> > 7 -1.00 343.41 -1093.34 335.74 335.74
> > 8 1.01 339.07 -1084.93 345.65 355.92
> > 9 0.99 353.07 -1065.54 355.92 345.65
> >10 1.01 372.93 -1033.57 366.56 377.59
> >11 0.99 382.02 -1008.65 377.59 366.56
> >12 1.02 377.76 -953.36 389.04 400.94
> >13 0.99 390.95 -917.41 400.94 389.04
> >14 -1.00 416.09 -940.33 413.26 413.26
> >15 -1.00 436.51 -914.99 426.10 426.10
> >16 1.02 447.63 -907.43 439.45 453.33
> >17 0.98 468.06 -901.60 453.33 439.45
> >18 1.02 463.97 -834.29 467.80 482.86
> >19 0.98 497.85 -823.69 482.86 467.80
> >20 -1.00 519.60 -810.16 498.57 498.57
> >21 -1.00 522.48 -750.48 514.99 514.99
> >22 1.02 534.13 -717.60 532.15 550.16
> >23 0.98 557.11 -697.81 550.16 532.15
> >24 1.02 557.72 -621.36 569.05 588.89
> >25 0.98 603.58 -628.77 588.89 569.05
> >26 -1.00 626.72 -610.91 609.73 609.73
> >27 -1.00 631.88 -557.24 631.72 631.72
> >28 -1.00 655.15 -519.64 654.96 654.96
> >
> >
> >Here is the remlog file without nmr constrints at 800th exchange step for comparison, for which the exchange behavior is normal since the temperature changes randomly.
> >
> > # exchange 800
> > 1 1.01 318.60 -1102.09 326.15 335.74
> > 2 0.99 350.53 -1069.53 355.92 345.65
> > 3 -1.00 451.63 -876.29 453.33 453.33
> > 4 0.99 303.18 -1179.28 299.31 290.95
> > 5 -1.00 643.10 -498.55 654.96 654.96
> > 6 0.99 342.37 -1093.50 335.74 326.15
> > 7 0.98 490.26 -862.57 482.86 467.80
> > 8 0.98 438.36 -928.33 426.10 413.26
> > 9 1.02 476.75 -843.67 467.80 482.86
> >10 -1.00 457.26 -935.72 439.45 439.45
> >11 0.99 412.27 -986.93 400.94 389.04
> >12 -1.00 281.33 -1210.95 282.86 282.86
> >13 0.99 317.90 -1142.84 316.90 307.97
> >14 -1.00 509.59 -803.96 498.57 498.57
> >15 1.02 518.21 -697.11 532.15 550.16
> >16 -1.00 607.03 -607.92 609.73 609.73
> >17 -1.00 636.50 -544.03 631.72 631.72
> >18 1.02 562.42 -648.02 569.05 588.89
> >19 1.02 405.12 -908.61 413.26 426.10
> >20 1.01 292.57 -1187.45 290.95 299.31
> >21 1.01 342.05 -1057.49 345.65 355.92
> >22 1.01 317.24 -1168.96 307.97 316.90
> >23 0.98 571.48 -702.44 550.16 532.15
> >24 0.98 598.90 -638.77 588.89 569.05
> >25 0.99 392.29 -1046.75 377.59 366.56
> >26 -1.00 514.00 -758.40 514.99 514.99
> >27 1.01 364.82 -1018.64 366.56 377.59
> >28 1.02 390.34 -988.70 389.04 400.94
> >
> >
> >Any suggestion and comments will be greatly appreciated.
> >
> >Thank you in advance!
> >
> >With all my whises,
> >Wenfei Li
> >
> >NJU, PRC
> >-----------------------------------------------------------------------
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