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专业: 理论和计算化学

[求助] gromacs单点能运行不下去

我想gromacs对某一特定构型进行单点能量的计算，我的体系就是一个弱键化合物周围有40个水分子，可是当我计算的时候，就出现下面的错误，无法进行下去。
NOTE 1 [file test.top, line 49]:
  Zero-step energy minimization will alter the coordinates before
  calculating the energy. If you just want the energy of a single point,
  try zero-step MD (with unconstrained_start = yes). To do multiple
  single-point energy evaluations of different configurations of the same
  topology, use mdrun -rerun.

Analysing residue names:
There are:    1    Other residues
There are: 50    Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 474.00
Largest charge group radii for Van der Waals: 0.330, 0.179 nm
Largest charge group radii for Coulomb:    0.330, 0.237 nm

WARNING 2 [file test.mdp]:
  The sum of the two largest charge group radii (0.567054) is larger than
  rlist (0.500000)

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 12x12x12, spacing 0.113 0.102 0.103
Estimate for the relative computational load of the PME mesh part: 0.55

NOTE 2 [file test.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

This run will generate roughly 0 Mb of data

There were 2 notes

There were 2 warnings

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1584

Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
请问该如何解决？
另外，我的弱键化合物是NH3....CH3BR，我自己写的top文件，只定义了键长和健角，请问对于这种弱键化合物，还存在pairs相互作用吗？请大家指点，在此谢过

[ Last edited by ghcacj on 2011-11-30 at 08:05 ]

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