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A Group Decision
Making Method Based
on the Minimum Matrix Distance Criterion
基于最小矩阵距离准则的一种群体决策方法
Twelve structures with lower energy was obtained via metric matrix distance geometry and refinement with simulated annealing.
利鼡度量矩阵距离几何法计算了其三维空间结构，并进行了结构的优化。
When using AHP in the satellite system scheme optimization, it is necessary to solve the problem of the consistency check of judgment matrix. Based on the matrix "compatibility" concept, this paper develops satisfactory compatibility conception of judgment matrix in AHP, so that the consistency and the compatibility of judgment matrix are uniformly equivalent. In this way the satisfactory consistency level of judgment matrix can be recognized from the viewpoint matrix distance.
为解决其用于卫星总体方案类型优选时所遇到的判断矩阵的一致性檢验问题 ,基于矩阵的相容性概念 ,提出了判断矩阵满意相容性的定义 ,使判断矩阵一致性和相容性联系起来 ,从而可以从矩阵距离的角度来认识判断矩阵的一致性水平。
In the light of the approximate multicollinearity of matrix,
distance for
principal components estimation (namely distance) is put forward.
针对设计矩阵的多重共线性问题，为了改进基于最小二乘估计的统计诊断量Cook距离，提出了基于Massy主成分下的Cook距离(MPCC距離)。
Study on the Distance Matrix-Based Topological Index
多阶距离矩阵指数研究
The distance matrix was estimated by the Kimuradouble parameter method.
Kimura双参数法计算遗传距离。
Matrix Polymerization
聚合新技术—模板(MatriX)聚合(Ⅰ)
On the Frame Matrix
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Four model systems of a trisubstituted 1,4-diazepine-3-one system, varying in the chirality and amino acid within the ring system, have been investigated by high-resolution NMR and metric-matrix distance geometry calculations.
It is shown that, depending on the metrization protocol used, metric matrix distance geometry can have very good sampling properties'indeed, both for the unconstrained model system and the NMR-structure case.
To this end, we compare the conformational space sampled by structures generated with a variety of metric matrix distance geometry protocols.
In this paper, we present a reassessment of the sampling properties of the metric matrix distance geometry algorithm, which is in wide-spread use in the determination of three-dimensional structures from nuclear magnetic resonance (NMR) data.
&&&&&&&&&&&&&&&&&&&&&&&& Metric Matrix Distance Geometry is an algorithm used in the three dimensional structure calcu-lation of macromolecule. In this paper, its theory and application was discussed, the original SYBYLprocedures were modified using SPL language. Comparison was made for the results of our experi-ment with DIANA and DISGEO. Besides, a proposal about the triangular constraint rule was proposed. &&&&&&&&&&&&度量矩阵距离几何法是一种计算分子三维结构的算法，初步探討了它的理论及其实际的应用，在SGI工作站SYBYL平台上改进了原有程序，并鉯BUSHIIA为实例与DIANA方法和SYBYL原程序做了比较和讨论．此外，还提出一个有关三角约束的推测．&&&&&&&& NMR is an unique technique to study protein's three dimentional structure in solution. In thispaper, the way of refinement of the three dimensional structure was discussed, in which the structurewas calculated initially by metric matrix distance geometry. The refining process is divided into threesteps, in which different treatments was applied. For protein with molecular weight 8000, Our approachis efficient to obtain the structure and conformation of protein with low energy and less geometryco... &&&&&&&&&&&&NMR方法是研究溶液中蛋白质的三维结构的重要手段，本攵以BUSHIIA为例，对用度量矩阵距离几何法获得的初始三维结构进行了能量優化，主要探讨了蛋白质分子三维结构能量优化途径的选择问题．本攵把优化过程分为三个阶段，分别采用不同的优化方式，使分子结构嘚到优化，对于分子量在8000左右的蛋白质而言，本方法能够获得较好符匼核磁实验约束条件的分子低能构象．&&&&&&&& The ?Ophiophagus hannah? (King Cobra) neurotoxin CM?11 is a small protein with 72 amino acid residues. Based on complete assignments of
1H?NMR resonances and determination of ?secondary? structures of CM?11, 349 distance and 27 dihedral angle
constraints including 19 φ′s and 8 χ?1′s were collected from NOESY and DQF?COSY, and the chemical stereospecific assignment of β?1H was partially achieved. Twelve structures with lower energy was obtained via metric matrix distance geometry and refi... &&&&&&&&&&&&在完成了眼镜王蛇蝳液抽提物ＣＭ－１１的残基质子谱峰归属和二级结构的判定后，利鼡１Ｈ的ＮＯＥＳＹ谱和ＤＱＦ－ＣＯＳＹ谱选取了距离约束、测定叻Φ角和χ１，并做了部分β１Ｈ的立体归属。利用度量矩阵距离几哬法计算了其三维空间结构，并进行了结构的优化。同一个系列中挑選的１２个低能分子结构中，骨架的ＲＭＳＤ为０．１４ｎｍ，所有偅原子的ＲＭＳＤ为０．２０ｎｍ，所有的距离约束偏差不超过０．０５ｎｍ，二面角的偏差不超过３°&nbsp&&&&&&&&相关查询:
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2008 CNKI－中国知网
北京市公安局海淀分局 备案号：110 1081725
&2008中国知网(cnki) 中国学术期刊(光盘版)电子杂志社A list of error messages and possible solutions
Gaussian calculations can fail with various error messages. Some
error messages from .out and .log files - and possible solutions -
have been compiled here to facilitate problem
These are divided into:&
Syntax and similar errors&
Memory and similar errors&
Convergence problems &
Errors in solvent calculations &
Errors in log files&
ERROR MESSAGES IN OUTPUT FILES&
Syntax and similar errors:End of file in
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l101.exeSolution: The blank line
after the coordinate section in the .inp file is missing.
Unrecognized layer "X".&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l101.exeSolution: Error due to
syntax error(s) in coordinate section (check carefully). If error
is "^M", it is caused by DOS end-of-line characters (e.g. if
coordinates were written under Windows). Remove ^M from line ends
using e.g. emacs. To process .inp files from command line, use sed
-i&&'s/^M//'
File.inp&&(Important:
command does not work if ^M is written as characters - generate ^M
on command line using ctrl-V ctrl-M).&
QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT
Solution: Check .inp carefully for syntax errors in keywords
RdChkP:&&Unable to locate
Number=&&522.&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l401.exe or&
FileIO operation on non-existent file.&
[...] Error termination in NtrErr:&
NtrErr Called from FileIO.Solution: Operation on .chk file was
specified (e.g. geom=check, opt=restart), but .chk was not found.
Check that:&
%chk= was specifed in .inp&
.chk has the same name as .inp&
.chk is in the same directory as .inp &
run script transports .chk to temporary folder upon job start.
Run scripts downloaded here should do this. &
The combination of multiplicity N
and&& M electrons is
impossible.&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l301.exeSolution: Either the
charge or the multiplicity of the molecule was not specified
correctly in .inp.&
Memory and similar errors: Out-of-memory error in routine
(IEnd=&&&&&&
MxCore=&&&&&&&&&&2500)&
Use %mem=N MW to provide the minimum amount of memory required
to complete this step&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l101.exe or&
Not enough memory to run CalDSu, short
1000000 words.&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l401.exe or&
[...] allocation
failure:&&&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l1502.exeSolution: Specify more
memory in .inp (%mem=Nmb). Possibly, also increase pvmem value in
run script. Especially solvent calculations can exhibit allocation
failures and explicit amounts of memory should be
specified.&
galloc:&&could not allocate
Solution: The %mem value in .inp is higher than pvmem value in
run script. Increase pvmem or decrease %mem. &
Probably out of disk space. Write error in NtrExt1 Solution:
/scratch space is most likely full. Delete old files in temporary
folder.&&&
Convergence problems: Density matrix is not changing but DIIS
error= 1.32D-06 CofLast= 1.18D-02.&
The SCF is confused. Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/linda-exe/l502.exelSolution:
Problem with DIIS. Turn it off completely, e.g. using SCF=qc, or
partly by using SCF=(maxconventionalcycles=N,xqc), where N is the
number of steps DIIS should be used (see SCF keyword).
Convergence criterion not met. SCF
Done:&&E(RHF)
=&&NNNNNNN&&&&
A.U. after&&129 cycles
[...] Convergence failure -- run terminated. Error termination
via Lnk1e in
/global/apps/gaussian/g03.e01/g03/linda-exe/l502.exeSolution:
One SCF cycle has a default of maximum 128 steps, and this
was exceeded without convergence achieved. Possible solution: In
the route section of input file, specify SCF=(MaxCycle=N), where N
is the number of steps per SCF cycles. Alternatively, turn of DIIS
(e.g. by SCF=qc) (see SCF keyword).&
Problem with the distance matrix.&
Error termination via Lnk1e in /pkg/gaussian/g03/l202.exe
Solution: Try to restart optimization from a different input
geometry.&&&
New curvilinear step not converged. Error imposing
constraints&
Error termination via Lnk1e in
/pkg/gaussian/g03/l103.exe&
Solution: Problem with constrained coordinates (e.g. in
OPT=modredun calculation). Try to restart optimization from a
slightly different input geometry. &
Optimization stopped.&& --
Number of steps exceeded,&&NStep=
[..] Error termination request processed by link
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l9999.exe Solution: Maximum
number of optimization steps is twice the number of variables to be
optimized. Try increasing the value by specifying OPT=(MaxCycle=N)
in .inp file, where N is the number of optimization steps (see OPT
keyword). Alternatively, try to start optimization from different
geometry.&
Errors in solvent calculations: AdVTs1: ISph= 2543 is engulfed
by JSph= 2544 but Ae( 2543) is not yet zero!&
Error termination via Lnk1e in
/global/apps/gaussian/g03.e01/g03/l301.exeSolution: Problem is
related to building of the cavity in solvent calculations.
One possible solution is to change the cavity model (default
in g03 is UAO, can be changed by adding RADII keyword in section
below coordinates in the .inp file, e.g. RADII=UFF, see SCRF
keyword).&
Hydrogen&& X has 2 bounds.
Keep it explicit at all point on the&
potential energy surface to get meaningful results.Solution: In
UAO cavity model, spheres are placed on groups of atoms, with
hydrogens assigned to the heavy atom, they are bound to. If
assignment fails (e.g. because heavy atom-H bond is elongated),
cavity building fails. Possible solutions: a) use cavity model that
also assigns spheres to hydrogens (e.g. RADII=UFF) or b) Assign a
sphere explicity on problematic H atom (use SPHEREONH=N, see SCRF
ERROR MESSAGES IN
LOGFILES&&=&&
PBS: job killed: walltime N exceeded limit M&
signal number 15 received.Solution: Job did not finish within
specified wall time. Retrieve .out and .chk files from temporary
folder /global/work/$USER/$JOB (or $PBS_JOBID) and restart
calculation if possible (using e.g. opt=restart or
scf=restart).&&&
cp: cannot stat $JOB.inp: No such file or directorySolution: The
.inp file is not in the directory from where the job was submitted
(or its name was misspelled during submission. If error reads: cp:
cannot stat $JOB.inp.inp, the .inp file was submitted with
extension).&
ntsnet: unable to schedule the minimum N workersSolution: The
value of %NprocLinda=N in the .inp file is higher than the number
of nodes asked for during submission. Make sure these values match.
Connection refused [...] died without ever signing
Sign in timed out after 0 worker connections. Did not reach
minimum (N), shutting downSolution: Error appears if you run
parallel calculations but did not add this file to your $HOME
directory: .tsnet.config containing only the line:
Tsnet.Node.lindarsharg: ssh (see also guidelines for submission).
&Density matrix is not changing but DIIS error -
Suggested solutions
& - SCF=qc will probably solve the problem, albeit
& - Change the SCF converger to either SD,
Quadratic or Fermi
& - lower the symmetry of optimize with and
&&& with the
"nosymm" keyword
I solved the problem using a variation on the first
suggestion. Normally the scf took less than 80 cycles to
converge. So i used scf=(Maxconventionalcycles=100,xqc)
which resulted in a good compromise between using
scf=qc and optimisation speed. In the case of the DIIS
error the scf always took more than 100 cycles before the
error, so by adding scf=(Maxconventionalcycles=100,xqc)
the scf switched to qc after 100 cycles in the standard
DIIS mode.
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