g_mmpbsa能量分解过程中的异常值

510426762 · 发表于 Post on 2018-3-17 04:16:00

本帖最后由 510426762 于 2018-3-17 06:47 编辑

模拟了蛋白质和受体在0.15M NaCl水溶液环境中的结合作用，时间长度100ns。rmsd结果稳定了。
g_mmpbsa分解能量，用的一步法分解，参数如下。

;Polar calculation: "yes" or "no"
polar = yes
;=============
;PSIZE options
;=============
;Factor by which to expand molecular dimensions to get coarsegrid dimensions.
cfac = 1.5
;The desired fine mesh spacing (in A)
gridspace = 0.5
:Amount (in A) to add to molecular dimensions to get fine grid dimensions.
fadd = 5
;Maximum memory (in MB) available per-processor for a calculation.
gmemceil = 4000
;=============================================
;APBS kwywords for polar solvation calculation
;=============================================
;Charge of positive ions
pcharge = 1
;Radius of positive charged ions
prad = 0.95
;Concentration of positive charged ions
pconc = 0.150
;Charge of negative ions
ncharge = -1
;Radius of negative charged ions
nrad = 1.81
;Concentration of negative charged ions
nconc = 0.150
;Solute dielectric constant
pdie = 2
;Solvent dielectric constant
sdie = 80
;Reference or vacuum dielectric constant
vdie = 1
;Solvent probe radius
srad = 1.4
;Method used to map biomolecular charges on grid. chgm = spl0 or spl2 or spl4
chgm = spl4
;Model used to construct dielectric and ionic boundary. srfm = smol or spl2 or spl4
srfm = smol
;Value for cubic spline window. Only used in case of srfm = spl2 or spl4.
swin = 0.30
;Numebr of grid point per A^2. Not used when (srad = 0.0) or (srfm = spl2 or spl4)
sdens = 10
;Temperature in K
temp = 300
;Type of boundary condition to solve PB equation. bcfl = zero or sdh or mdh or focus or map
bcfl = mdh
;Non-linear (npbe) or linear (lpbe) PB equation to solve
PBsolver = lpbe
;========================================================
;APBS kwywords for Apolar/Non-polar solvation calculation
;========================================================
;Non-polar solvation calculation: "yes" or "no"
apolar = yes
;Repulsive contribution to Non-polar
;===SASA model ====
;Gamma (Surface Tension) kJ/(mol A^2)
gamma = 0.0226778
;Probe radius for SASA (A)
sasrad = 1.4
;Offset (c) kJ/mol
sasaconst = 3.84928
;===SAV model===
;Pressure kJ/(mol A^3)
press = 0
;Probe radius for SAV (A)
savrad = 0
;Offset (c) kJ/mol
savconst = 0
;Attractive contribution to Non-polar
;===WCA model ====
;using WCA method: "yes" or "no"
WCA = no
;Probe radius for WCA
wcarad = 1.20
;bulk solvent density in A^3
bconc = 0.033428
;displacment in A for surface area derivative calculation
dpos = 0.05
;Quadrature grid points per A for molecular surface or solvent accessible surface
APsdens = 20
;Quadrature grid spacing in A for volume integral calculations
grid = 0.45 0.45 0.45
;Parameter to construct solvent related surface or volume
APsrfm = sacc
;Cubic spline window in A for spline based surface definitions
APswin = 0.3
;Temperature in K
APtemp = 300

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计算出来的能量，发现energy_MM里有异常值。主要集中在s4 s5 s6,Protein-MOL VdW Energy接近于0，VdW = s4 - s0 - s2

@ s0 legend "Protein VdW Energy"
@ s1 legend "Protein Elec. Energy"
@ s2 legend "MOL VdW Energy"
@ s3 legend "MOL Elec. Energy"
@ s4 legend "Protein-MOL VdW Energy"
@ s5 legend "Protein-MOL Elec. Energy"
@ s6 legend "Protein-MOL Total Energy"
0.000 0.000 0.000 0.000 0.000 -0.001 -0.342 -0.343
100.000 0.000 0.000 0.000 0.000 -0.001 -0.437 -0.438
200.000 0.000 0.000 0.000 0.000 -278.876 -37.203 -316.079
300.000 0.000 0.000 0.000 0.000 -286.627 -43.203 -329.830
400.000 0.000 0.000 0.000 0.000 -0.001 -0.025 -0.025
500.000 0.000 0.000 0.000 0.000 -307.671 3.073 -304.598
600.000 0.000 0.000 0.000 0.000 -285.399 -26.875 -312.274
700.000 0.000 0.000 0.000 0.000 -0.001 0.014 0.013
800.000 0.000 0.000 0.000 0.000 -0.001 -0.132 -0.133
900.000 0.000 0.000 0.000 0.000 -0.001 0.037 0.036
1000.000 0.000 0.000 0.000 0.000 -0.001 0.319 0.318
1100.000 0.000 0.000 0.000 0.000 -0.001 0.156 0.155
1200.000 0.000 0.000 0.000 0.000 -0.001 0.322 0.321
1300.000 0.000 0.000 0.000 0.000 -260.126 -5.969 -266.095
1400.000 0.000 0.000 0.000 0.000 -0.001 -0.495 -0.496
1500.000 0.000 0.000 0.000 0.000 -0.001 -0.023 -0.023
1600.000 0.000 0.000 0.000 0.000 -0.001 -0.141 -0.142
1700.000 0.000 0.000 0.000 0.000 -0.001 -0.035 -0.035
1800.000 0.000 0.000 0.000 0.000 -0.001 -0.068 -0.069
1900.000 0.000 0.000 0.000 0.000 -0.001 0.088 0.088
2000.000 0.000 0.000 0.000 0.000 -264.009 -3.774 -267.782
2100.000 0.000 0.000 0.000 0.000 -0.001 -0.227 -0.227
2200.000 0.000 0.000 0.000 0.000 -0.001 0.137 0.136
2300.000 0.000 0.000 0.000 0.000 -0.001 -0.138 -0.139
2400.000 0.000 0.000 0.000 0.000 -0.001 0.105 0.105
2500.000 0.000 0.000 0.000 0.000 -0.001 0.039 0.038

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这个算作异常值么？还是由于这个时刻蛋白质和配体的确没有VdW力作用了呢？

大概情况如上

510426762 · 发表于 Post on 2018-3-17 05:10:05

好像可能解决了。
看到这篇帖子提示了。http://bbs.keinsci.com/thread-6822-1-1.html
g_mmpbsa里也说明了
WARNING: Trajectory should be PBC corrected and molecule should not be PBC broken. To make molecule whole in trajectory, please follow these links: PBC and trjconv.

HarrisLin · 发表于 Post on 2018-3-26 14:55:13

本帖最后由 HarrisLin 于 2018-3-26 14:58 编辑

是PBC的問題沒錯要用noPBC分析

510426762 · 发表于 Post on 2018-5-30 11:56:19

510426762 发表于 2018-3-17 05:10
好像可能解决了。
看到这篇帖子提示了。http://bbs.keinsci.com/thread-6822-1-1.html
g_mmpbsa里也说明 ...

是的，之后仔细阅读，发现漏掉了这句。
用这种方式做了noPBC
echo "0" | gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_whole.xtc -pbc whole -n index.ndx
echo "1 0" | gmx trjconv -s md_0_1.tpr -f md_0_1_whole.xtc -o md_0_1_mol_center.xtc -center -pbc mol -n index.ndx

lonemen · 发表于 Post on 2018-9-14 18:28:23

学习了，并收藏之。

芮啦 · 发表于 Post on 2021-6-4 10:27:32

510426762 发表于 2018-3-17 05:10
**** 作者被禁止或删除内容自动屏蔽 ****

我现在刚开始学习使用g_mmpbsa来计算结合能，有一点问题希望向您请教一下，请问您的mdp参数文件是采用官网上的参数还是依照自己的体系设定的呢，我的体系中不止有一种阳离子，所以在设定mdp文件中的pcharge、prad等参数时不知道怎么处理，希望向您请教一下，还请您指点一二

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[GROMACS] g_mmpbsa能量分解过程中的异常值

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