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bay__gulf金虫 (著名写手)
刘苏州
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【在线答疑】关于NAMD/VMD 已有27人参与
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
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Bay兄好，我在进行一个含有NAD的脱氢酶的分子动力学模拟，利用VMD进行PSF文件的准备，整个过程是这样的，利用Pymol加氢，在TOP文件中除了默认的那个之外还加上了toppar_all27_na_nad.ppi.str,加水盒，再写NAMD的CONFIG文件时，par文件同样加上了toppar_all27_na_nad.ppi.str，可是在最后的运行中出现了能量最小化无法进行，问题程序如下： D:\namd>namd2 BphBW.namd Charm++: standalone mode (not using charmrun) Info: NAMD 2.6 for Win32-i686 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 D:/namd/BphBW.dcd Info: DCD FREQUENCY 50 Info: DCD FIRST STEP 50 Info: XST FILENAME D:/namd/BphBW.xst Info: XST FREQUENCY 50 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME D:/namd/BphBW Info: RESTART FILENAME D:/namd/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 1269358131 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB D:/namd/BphBW.pdb Info: STRUCTURE FILE D:/namd/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/stream/toppar_all27_na_nad_ppi.str 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 Info: SKIPPING rtf SECTION IN STREAM FILE Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT Info: SUMMARY OF PARAMETERS: Info: 307 BONDS Info: 769 ANGLES Info: 1254 DIHEDRAL Info: 81 IMPROPER Info: 6 CROSSTERM Info: 190 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 0.0200817 -0.00200932 -0.0315461 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 在这里就进行不下去，推测原因如程序中提到的，增大CUTOFF值貌似也不好用，请Bay兄指点一下可能的原因~谢谢 |
143楼2010-03-23 23:40:57
2楼2009-05-02 11:58:42
bay__gulf
金虫 (著名写手)
刘苏州
- 模拟EPI: 8
- 应助: 9 (幼儿园)
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- 帖子: 1344
- 在线: 271小时
- 虫号: 592012
- 注册: 2008-09-03
- 专业: 理论和计算化学
- 管辖: 分子模拟
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lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
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【回2楼】 可以，比如下面这篇文献 Bryan J. Johnson, Jordi Cohen, Richard W. Welford, Arwen R. Pearson, Klaus Schulten, Judith P. Klinman, and Carrie M. Wilmot. Exploring molecular oxygen pathways in Hanseluna Polymorpha copper-containing amine oxidase. Journal of Biological Chemistry, 282:17767-17776, 2007. [ Last edited by bay__gulf on 2009-5-2 at 13:21 ] |
3楼2009-05-02 13:13:06
4楼2009-05-02 13:45:28