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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » Gromacs/Amber/NAMD » 【求助】namd能量最小化时出现问题，求指教
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zh1987hs

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[交流] 【求助】namd能量最小化时出现问题，求指教 已有3人参与

在运行NAMD时出现问题，因为酶中含有FAD，在TOPLOGY文件时除了默认文件外，又加了top_all27_prot.rtf,在PARAMETER文件选择时没有加额外的文件，运行能量最小化时出错，运行如下：请各位虫友指教可能的原因：

C:\Documents and Settings\Administrator>D:

D:\>cd namd

D:\namd>namd2 BphBW.namd
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Win32-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd@ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-win32-smp
Info: Built Wed Aug 30 14:13:15 2006 by administrator on malta
Info: Running on 1 processors.
Info: 0 kB of memory in use.
Info: Memory usage based on nothing
Info: Configuration file is BphBW.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             4000 steps
Info: FIRST LDB TIMESTEP     100
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    50
Info: MAX PAIR PARTITIONS    20
Info: SELF PARTITION ATOMS   125
Info: PAIR PARTITION ATOMS   200
Info: PAIR2 PARTITION ATOMS  400
Info: MIN ATOMS PER PATCH    100
Info: INITIAL TEMPERATURE    298
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           BphBW.dcd
Info: DCD FREQUENCY          50
Info: DCD FIRST STEP         50
Info: XST FILENAME           BphBW.xst
Info: XST FREQUENCY          50
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        BphBW
Info: RESTART FILENAME       BphBW.restart
Info: RESTART FREQUENCY      1000
Info: SWITCHING ACTIVE
Info: SWITCHING ON           9
Info: SWITCHING OFF          10
Info: PAIRLIST DISTANCE      12
Info: PAIRLIST SHRINK RATE   0.01
Info: PAIRLIST GROW RATE     0.01
Info: PAIRLIST TRIGGER       0.3
Info: PAIRLISTS PER CYCLE    2
Info: PAIRLISTS ENABLED
Info: MARGIN                 0
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        14.5
Info: ENERGY OUTPUT STEPS    100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED     1269347840
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         BphBW.pdb
Info: STRUCTURE FILE         BphBW.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             D:/Program Files/University of Illinois/VMD/plugins
/noarch/tcl/readcharmmpar1.1/par_all27_prot_lipid_na.inp
Info: PARAMETERS             D:/namd/toppar/toppar_history/c34b2/par_all22_prot.
inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 446 BONDS
Info: 1114 ANGLES
Info: 1706 DIHEDRAL
Info: 124 IMPROPER
Info: 6 CROSSTERM
Info: 285 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 57466 ATOMS
Info: 39760 BONDS
Info: 25471 ANGLES
Info: 11235 DIHEDRALS
Info: 692 IMPROPERS
Info: 279 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 172395 DEGREES OF FREEDOM
Info: 19860 HYDROGEN GROUPS
Info: TOTAL MASS = 349765 amu
Info: TOTAL CHARGE = -5 e
Info: *****************************
Info: Entering startup phase 0 with 0 kB of memory in use.
Info: Entering startup phase 1 with 0 kB of memory in use.
Info: Entering startup phase 2 with 0 kB of memory in use.
Info: Entering startup phase 3 with 0 kB of memory in use.
Info: PATCH GRID IS 5 BY 8 BY 6
Info: REMOVING COM VELOCITY -0.00209524 -0.0153317 0.00235918
Info: LARGEST PATCH (101) HAS 340 ATOMS
Info: CREATING 4195 COMPUTE OBJECTS
Info: Entering startup phase 4 with 0 kB of memory in use.
Info: Entering startup phase 5 with 0 kB of memory in use.
Info: Entering startup phase 6 with 0 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 0 kB of memory in use.
Info: CREATING 4195 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 1.69407e-021 AT 9.89634
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.52418e-014 AT 9.94673
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 8.47033e-022 AT 9.94673
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 6.77309e-016 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.57772e-030 AT 9.89634
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 4.54938e-015 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 5.91646e-031 AT 9.94673
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 5.6823e-016 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.71751e-025 AT 9.94673
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 1.45371e-014 AT 9.94673
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 6.20385e-025 AT 9.94673
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97512e-016 AT 9.94673
Info: Entering startup phase 8 with 0 kB of memory in use.
Info: Finished startup with 0 kB of memory in use.
TCL: Minimizing for 1000 steps
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP
          ELECT            VDW       BOUNDARY           MISC        KINETIC
          TOTAL           TEMP         TOTAL2         TOTAL3        TEMPAVG

ENERGY:       0   5244966.2491        -1.#IND         1.#QNB         1.#QNB
   -199915.8640  99999999.9999         0.0000         0.0000         0.0000
         1.#QNB         0.0000         1.#QNB         1.#QNB         0.0000

OPENING EXTENDED SYSTEM TRAJECTORY FILE
INITIAL STEP: 1e-006
GRADIENT TOLERANCE: 1.#QNAN
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1楼 2010-03-23 20:44:15
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wu3833145

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等待大牛来解答啊
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2楼2010-04-10 10:52:20
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bay__gulf

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刘苏州
★ ★
lei0736(金币+2):谢谢 2010-04-10 12:11
zh1987hs(金币+5):谢谢~我在琢磨琢磨 2010-04-10 12:47
1 参数有误
2 构型有误(极可能)
3 PBC 有误
具体是哪个, 我们大家一起猜
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3楼2010-04-10 11:38:12
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superdirac

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★ ★ ★
zh1987hs(金币+2):谢谢~ 2010-04-18 21:39
lei0736(金币+3):谢谢 欢迎常来 2010-04-18 22:25
１
Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107 k_ub=0 r_ub=0
   USING VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0

你的参数文件有问题。有一个参数的类型设了两次。

２
Warning: Increasing cutoff during minimization may avoid this.
　　体系中的原子运动的太快。
　　steppercycle　改小一点。　

[ Last edited by superdirac on 2010-4-18 at 17:55 ]
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我认为，酒一口一口喝，路一步一步走~步子迈大了，喀~容易扯着蛋
4楼2010-04-18 17:45:39
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