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关于用amber跑REMD计算的流程及输入文件的设置
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最近看了一篇论文，http://www.ncbi.nlm.nih.gov/pubmed/22339436 作者使用amber做了REMD（replica exchange molecular dynamic）的计算。 自己正好也有类似需要，想用REMD模拟。就想按论文相同的条件实现一下，不过论文里的过程写的不是很详细。下面是原文的method部分： In this work, the temperature setting used for sheep PrP 125-230 such that MD simulations were exchanged at 320.0, 322.0,324.0, 326.0, 328.1, 330.2, 332.3, 334.4, 336.5, 338.6, 340.8, 343.0, 345.2, 347.4, 349.6, 351.8, 354.0, 356.2, 358.5, 360.8, 363.1, 365.4, 367.7, and 370.0 K was used. All of the replicas were equilibrated for 20 ns without exchanging temperatures and then extended for 65 ns of REMD simulation. The generalized Born model used in this study modified the calculation of Born radii and improved the accuracy in the solvent polarization for macromolecules. The combinational use of the all-atom point-charge force-field (also known as ff03) and the generalized Born model led to successful folding of several proteins. The AMBER 11 simulation package 26 was used in both REMD simulation and data analysis. The melted huPrP 121-230 was computed starting from an extended huPrP. To generate the initial extended structure, a heating method was applied to a known NMR structure (PDBcode 1hjn,15Figure 1A), enabling it to unfold at 600 K for 40 ns of MD simulation to result in an extended conformation (Figure 1B) as described previously. During this simulation, the disulfide covalent bond between residues 179 and 214 was preserved. In total, 24 replicas with duration of 65 ns and with an integration time step of 2 fs were computed based on the extended huPrP with different random number seeds to generate the initial conditions. A 16 Å force-shifted non-bonded cutoff and generalized Born solvent models with salt concentration of 0.2 M were applied. 根据文章的描述我自己总结了一下，并按文章描述写了各个环节的输入文件。想和大家交流一下，看看我写的有没有不合适的问题。 Simulation Procedure: 1. system building 2. system minimization 3. heating system 4. generate the extend conformation 5. local minimization after heating system 6. equilibrate the every replica 7. REMD simulation 1.leap.inp for system building source pdb: 1ag2 use the the ff03 (Duan et al.) force field leap.inp source leaprc.ff03.r1 # load pdb file 1ag2 = loadPdb input.pdb # solvation # solvatebox 1ag2 TIP3PBOX 18.0 # save 1ag2 to pdb file savePdb 1ag2 1ag2.pdb # add countinos # addions 1ag2 Cl- 0 # addions 1ag2 Na+ # s-s bond bond 1ag2.179.SG 1ag2.214.SG # save 1ag2 to prmtop and inpcrd files saveAmberParm 1ag2 1ag2.prmtop 1ag2.inpcrd # finish quit 2. system minimization minimisation for heated system &cntrl imin=1, maxcyc=1000, ncyc=500, cut=999., rgbmax=999.,igb=1, ntb=0, ntpr=100 / ~ ~ 3. heat the system heating system from 0 K to 600K. &cntrl nstlim = 50000, dt = 0.002, ntt = 1, tautp = 1.0, tempi = 0, temp0 = 600, ntc =2, ntf = 2, ntpr =100, ntwx = 100, ntb = 0, igb = 1, #这里设置和后面remd的设置不同（igb = 5）结果可能受影响。 cut = 999.0,rgbmax = 999.0, / 4. generate the full unfolded conformation To generate the initial extend structure, a heating method was used to a known NMR structure (PDB code:1ag2), enabling it to unfold at 600 K for 40 ns of LD simulation to result in an extended conformation. 40nsld.inp enabling the heated NMR structure to unfold at 600 K for 40ns of LD simulation &cntrl irest = 1, ntx = 5, nstlim = 20000000, dt = 0.002, ntt = 3, gamma_ln = 1.0, tempi = 600,temp0 = 600, ntb = 0, igb = 2, ntpr = 500, ntwx = 1000, ntwr = 2000000, ntc = 2, ntf = 2, cut = 999.0,rgbmax = 999.0, / | RE_POSITION Moving by -2.485812 -1.096141 0.618430 NSTEP = 20000000 TIME(PS) = 40060.000 TEMP(K) = 577.57 PRESS = 0.0 Etot = 1351.4737 EKtot = 2407.9819 EPtot = -1056.5082 BOND = 626.4085 ANGLE = 1429.4823 DIHED = 1419.4285 1-4 NB = 376.4803 1-4 EEL = 3772.0639 VDWAALS = -368.8173 EELEC = -5949.1848 EGB = -2362.3695 RESTRAINT = 0.0000 ------------------------------------------------------------------------- A V E R A G E S O V E R ******* S T E P S NSTEP = 20000000 TIME(PS) = 40060.000 TEMP(K) = 600.20 PRESS = 0.0 Etot = 1514.3153 EKtot = 2502.2899 EPtot = -987.9746 BOND = 644.7390 ANGLE = 1506.2954 DIHED = 1362.4635 1-4 NB = 397.8849 1-4 EEL = 3727.1078 VDWAALS = -361.6498 EELEC = -5967.0181 EGB = -2297.7973 RESTRAINT = 0.0000 ------------------------------------------------------------------------- 结果Eptot 的plot图 600kmd.inp enabling the heated NMR structure to unfold at 600 K for 40ns of LD simulation &cntrl irest = 0, ntx = 1, nstlim = 20000000, dt = 0.002, ntt = 3, gamma_ln = 1.0, tempi = 600,temp0 = 600, ntb = 0, igb = 2, ntpr = 500, ntwx = 1000, ntwr = 2000000, ntc = 2, ntf = 2, cut = 999.0,rgbmax = 999.0, / 600kmd.out ... | RE_POSITION Moving by -0.033675 -0.790281 -1.085325 NSTEP = 2000000 TIME(PS) = 4060.000 TEMP(K) = 601.00 PRESS = 0.0 Etot = 1554.3820 EKtot = 2505.6360 EPtot = -951.2540 BOND = 654.9106 ANGLE = 1485.1469 DIHED = 1383.1021 1-4 NB = 422.1188 1-4 EEL = 3774.2620 VDWAALS = -379.3759 EELEC = -6038.4682 EGB = -2252.9505 RESTRAINT = 0.0000 ------------------------------------------------------------------------- A V E R A G E S O V E R 2000000 S T E P S NSTEP = 2000000 TIME(PS) = 4060.000 TEMP(K) = 599.90 PRESS = 0.0 Etot = 1513.2011 EKtot = 2501.0782 EPtot = -987.8771 BOND = 644.5795 ANGLE = 1506.1933 DIHED = 1361.8286 1-4 NB = 398.1118 1-4 EEL = 3724.2906 VDWAALS = -363.4705 EELEC = -5968.1047 EGB = -2291.3058 RESTRAINT = 0.0000 irest = 1, ntx = 5,和irest = 0, ntx = 1 模拟结过差别还是有的，从EPtot的结果来看，后者结构变化比较激烈，前者较稳定。但是不知道在这个模拟里用哪个合适？ 5. local minimization after heating system 使用第三步minimization的输入文件。 6. equilibrate the every replica equilibrate.mdin equilibration 20 ns, every 10ps save output. equilibration &cntrl irest=0, ntx=1, nstlim=10000000, dt=0.002, irest=0, ntt=3, gamma_ln=1.0, temp0=XXXXX, ig=RANDOM_NUMBER, ntc=2, ntf=2, nscm=1000, ntb=0, igb=5, cut=999.0, rgbmax=999.0, ntpr=5000, ntwx=5000, ntwr=10000000, nmropt=1, / &wt TYPE='END' / DISANG=system_chir.dat 7. REMD simulation remd 40ns exchange every 2ps <- 这里一直有困惑，到底间隔多久交换一下比较合适？ remd.mdin remd 40ns exchange every 2ps &cntrl irest=0, ntx=1, nstlim=1000, dt=0.002, irest=0, ntt=3, gamma_ln=1.0, temp0=XXXXX, ig=RANDOM_NUMBER, ntc=2, ntf=2, nscm=1000, ntb=0, igb=5, cut=999.0, rgbmax=999.0, ntpr=100, ntwx=1000, ntwr=100000, nmropt=1, numexchg=20000, / &wt TYPE='END' / DISANG=system_chir.dat |
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