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jackyma

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[交流] 关于用amber跑REMD计算的流程及输入文件的设置

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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1楼2013-07-02 11:40:08

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蓝洛水seven

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楼主，请问REMD计算完后，知道怎么分析RMSD吗

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7楼2013-10-13 15:59:59

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送红花一朵

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2楼2013-07-03 09:54:58

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irest = 1, ntx = 5,和irest = 0, ntx = 1 模拟结过差别还是有的，这个当然有差别，前者是指在前一次的基础上继续进行动力学模拟，而后者却是采用波尔兹曼函数来随机的产生初始速度，结果肯定是前者好啊。因为加热平衡根本联系不到一起了，结果又怎么可能会好

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3楼2013-07-04 09:18:13

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jackyma

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引用回帖:

3楼: Originally posted by 1054950560 at 2013-07-04 09:18:13
irest = 1, ntx = 5,和irest = 0, ntx = 1 模拟结过差别还是有的，这个当然有差别，前者是指在前一次的基础上继续进行动力学模拟，而后者却是采用波尔兹曼函数来随机的产生初始速度，结果肯定是前者好啊。因为加热平 ...

谢谢指点！

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4楼2013-07-09 14:25:43

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2013-07-09 14:25 回复

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2楼: Originally posted by 超人与小木虫 at 2013-07-03 09:54:58 希望能够与你交流交流！！！！