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【求助】namd能量最小化时出现问题，求指教 已有3人参与
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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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2楼2010-04-10 10:52:20
bay__gulf
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3楼2010-04-10 11:38:12
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
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
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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 ] |
4楼2010-04-18 17:45:39
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