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分子动力学模拟程序

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The MD program, v.4.3_beta, released 18 Nov 1998
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Authors:

Alexander Lyubartsev
Aatto Laaksonen 

Div. Physical Chemistry
Arrhenius Laboratory
Stockholm University
S 106 91   Stockholm
Sweden

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This program is a general purpose molecular dynamics code for simulations
of mixtures  of either rigid or flexible molecules, interacting by
AMBER-like force field in a periodic rectangular cell. In the case of 
flexible molecules the double time step algorithm is used.
Algotithms for NVE, NVT and NPT are employed, as well
as optimized Ewald sum for treatment of the electrostatic interactions. 
The program can be run both in sequential and parallel execution, in
the latter case the MPI parallel environment is required.    
                    
The program is originally based on the MOLDYN program by Aatto Laaksonen,
available from the CCP5 program library, Daresbury Lab, UK.
Since 1993 many additional changes were made by Alexander Lyubartsev, some
of these are:

NVT ensemble (v2.1)  

Essential reorganisation of force calculations (v2.4)

NPT ensemble (v3.0)            

optimization of Ewald summation (v.3.3)

complex DNA-like molecules (v3.5)                 

non-cubic (rectangular) cell (v3.6)

hydrogen bonds included (10-12 potential) (v3.7)

first parallel version (v3.8)    

universal code for sequential and parallel executions  (v3.9)

fully parallelized code, including particle moving (v4.0)

Different types of torsion potential, improper dihedrals, special
list of LJ interactions                             (v.4.1)

Other features in effect now:

Separate pressure controll in each direction
Reaction field method for electrostatic interactions
Hexagonal or truncated octahedral cells
Calculation of different energy contributions, radial distribution functions 
and time correlation functions during the execution.

The program was tested on:
        IBM-RISC 6000 system,
	IBM SP2 parallel computer 
	Cray T3E
	DEC Alpha
        PC-Pentium or Pentium Pro with Linux 1.3 or 2.0, f2c or g77 Fortran
	PGI (Portland group) Fortran for Linux or Windows NT

Parallel "Linux" version was tested for several PC connected via Ethernet
and also for a single PC with 2 processors.  

RAM Memory: depends on the simulated system, in the range 32-120 Mb 
for system 10**3-10**4 atoms


The present version should be considered as "BETA" 
Some bugs in the algorithm  may be still present.