changes

分子动力学模拟程序

v2.1
NVT ensemble (v2.1)  
Essential reorganisation of force calculations (v2.4)
NPT ensemble (v3.0)            
optimization of Ewald sum calculations (v3.3)
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) 

v4.0
- fully parallelized code, including particle moving
corrected small bug in calculations of type-type intermolecular energies.
(there were different weight from the short and long forces) 

v 4.1  
- new format on the input file (free format with commentaries instead
  of NAMELIST)
- slightly changed format of .mol files 
- readind of initial atom or molecular center of mass coordinates 
  from a file included 
- special LJ parameters for 1-4 intramolecular interactions   
- Morse potential for arbitrary bonds       
- Sum(cos(fi)**n) type of torsion potential (for hydrocarbon chains)
- Improper dihedral angles potential 

v.4.2

- improved memory-saving algorithm. All two-dimensionl arrays A(NS,NS)
where NS is the total number of different sites on molecules are removed 
without noteciable increasing of computation time.

- option for separate pressure control in each direction. 
Components Pxx,Pyy,Pzz of the pressure tenzor are coupled to the 
Nose-Hoover thermostat separately (non diagonal terms of the pressure 
tensor are supposed to be 0). Do not use the option for isotropic systems
in which nothing prevent the system to shrink the size in one direction and
increase it in another while keeping the volume (and pressure) constant.

- reaction field method for treatment of electrostatic interactions,
including "generalised reaction field" method for non-zero ionic strength
(I.G.Tironi, R.Sperb, P.E.Smith, W.F.van Gunsteren, 
J.Chem.Phys.,102,5451(1995))

- cell of truncated octahedron geometry:
  |x| < L/2 ; |y| < L/2 ;  |z| < L/2 ; |x|+|y|+|z| < 0.75*L

- cell oh hexagonal geometry

- If Ewald method for electrostatic interactions is not used, the list
of neighbours for atoms on small molecules (Natoms <= 5) is defined from
the distance between molecular centre-of-mass, that is the whole molecules 
occur within or out cut-off. In other cases, as before, list of neigbours
for each atom is determined from distances between the atoms. 

21.10.97  Bug in pressure calculations in the case of parallel implementation
of constrain dynamics (SHAKE) is removed.  

v.4.2 -> 4.3
------------

In v.4.3 most of the subroutines were essentially regrouped into new files
See details in file README
A lot of comments were inserted into the code.

The MD algorithm for NVT or NPT ensemble was rewritten 
according to "modular-invariant" version of the Nose-Hoover thermostat, see
 
  of G.J.Martyna, D.J.Tobais and M.L.Klein,
  J.Chem.Ohys., v.101(5), p.4177 (1994)
  
Some work has still to be done for the case of constrained dynamics 
(it works now, but not in the complete correspondence to the paper 
cited above)  


04.03.98  Several small bugs were corrected:
  in mpi.f procedure: addressing to NUMTASK (nonexistent) node which
sometimes happened in SINHR subroutine is removed
(this might cause crash of the program; otherwise it worked )
  in supl.f, TESTCONF - did not catch before all bad configurations
  "molecular" pressure in the double time step algorithm now calculated
correctly.
  Cray specific files were added  (mpi_cray.f, getcpucr.c and Makekefiles

12.04.98 A new possibility to add options in the input file is introduced:
  After lines defining unit vector (just before lines which defines RDFs)
  one can write
  
 add <n>

  where n is number of additional options. Then follows n lines defining
  additional options
  
  Now following extra options difined:
  
 inputf   - read restart file in ASCII format 
 outputf  - write restart file in ASCII format
 
 no aver  - do not calculate averagre bond lenghts, angles and torsions. 
            this may save a lot of memory while simulating large
	    macromolecules
	    
More detailed description of additional options is in file Extra_param 


11.01.99
  Option "Cut large forces" (see "MD.input")  is now working
  
22.02.99
  File prcm.h is divided into two parts:
  
  dimpar.h defines sizes of working arrays (may be customized)
  prcm.h - the rest of old prcm.h file (should not be changed)

26.04.99 
  Utility "makemol" to generate .mol files from "simple molecule file"
.smol and force field database is added. See Makemol.doc for details.

22.06.99 
  projections of time correlation functions may be now calculated both 
  in the laboratory and in the molecular priuncipal coordinate systems
  (flags 1 or 2 for corresponding tcf-s in the input file)
  
22.08.01
  Kong combination rules for Lennard-Jones cross-interactions are introduced
  (J. Kong, J.Chem.Phys., 59, 2464 (1973)). See ExtraParam file.
  
15.02.05
  Option for reading start-up configuration has changed.
  Value "0" now reads input coordinates in "XMOL" format while
  value "-2" reads atom coordinates as three columnns X Y Z with
  optional commentaries
  

v. 4.4    

  Possibility of separate Nose thermostat for each molecular species.
  Separate temperature control over species (Nose or velocity scaling) 
  is now switched on by extra parameter  "T-sep" (see file Extra_param) 

  Out-cutoff correction for energy and pressure now correct.
  It was too small (by factor between 2pi and 4pi) in older version

  Thermostat/barostat algorithm with constraint dynamics - algorithm
  rewritten. 

  XMOL trajectory file includes now information on the box sizes
  in the commentory lines
  
  Tranal:   now can read trajectories in MDynaMix binary format, XMOL format
  (provided second line contains time in fs) and PDB trajectories from GROMACS
  
  2005-12-01
  Expanded ensemble version of the program is updated (mdee). It not
  implements most of the features of MDynaMix except parallelization