AMBER Archive (2006)

Subject: AMBER: problem of the REMD with nmr constraints

From: wenfei Li (wfli_at_biophy.nju.edu.cn)
Date: Wed Nov 22 2006 - 19:57:32 CST

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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