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 02 September 2010

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Handy Routines for Ptraj (AmberTools 1.x and AMBER 9)

We (contact Hannes Loeffler for questions) have extended the functionality of the ptraj utility (AmberTools 1.x/AMBER9) to include some useful routines. A key feature of the diffusion and the mean residence time code is that it allows dynamic selection of regions (at the moment based on fixed distances between sets of atoms). The functions in detail are:

1. A mostly rewritten diffusion code.
2. Mean residence time calculations based on a) the survival function and b) the "standard" autocorrelation function [1-3]. (Alternative method described in selected reponses from the Amber mail reflector).
3. Calculation of the density along a coordiante useful for e.g. for membrane simulations. (Alternatively, the output of the grid command can be post-processed to get similar results.)
4. Calculation of order parameters for lipids in planar membranes.
5. Calculation of the pair-distance distribution function P(r).
6. A simple routine to calculate distances to nearest neighbour boxes.

The following three files contain the routines and header information.

1. actions.c contains the main routines
   1. transformDiffusion (modified diffusion code)
   2. transformMRT (mean residence time correlation functions)
   3. transformDensity (density along coordinate)
   4. transformOrderParameter (order parameters)
   5. transformPairDist (pair-distance distribution function P(r))
   6. transformImgDist (distances to neighbour images)
   and the helper functions calculateMSD, inout_MRT, increaseMem plus some basic vector routines. These functions need to be copied and pasted to the orginial actions.c from the distribution (simply appending the contents of the file provided here should be fine). The original function transformDiffusion should be commented out if the new one is to be used.
2. actions.h contains the header information for the routines above and needs to be copied and pasted to the orginial actions.h. Please note that the contents of the file provided here goes before the final #endif /* ACTION_MODULE */ (delete this final line from the original action.h and append).
3. version.h contains version information.

Updates

• Feb 18, 2010: The order command now optionally computes tail end-to-end distances.
• Feb 16, 2010: Order parameter calculations for lipids in planar membranes implemented.
• Feb 9, 2010: The diffusion command has now 'convenience' switches to calculate the MSD in only one, two, or all three dimensions. Data will be written in the last column of the output file. A simple Perl script is provided to compute window averages.
• Feb 1, 2010: The density command now optionally reads a file with electron numbers.

Code Modifications

The following modifications to the code are also required in addition to copying and pasting the contents of the files as described above to compile the code.

1. Prototypes for the new funcions and new enumeration types have to be added to action.h.

   typedef enum _actionType {
   .
   .
     TRANSFORM_MRT,
     TRANSFORM_DENSITY,
     TRANSFORM_PAIRDIST,
     TRANSFORM_IMGDIST,
     TRANSFORM_ORDERPARAMETER
   } actionType;
   .
   .
     extern int transform2dRMS(actionInformation *, 
                             double *, double *, double *, double *, int);
   
     /* the next four prototypes are new */
     extern int transformMRT(actionInformation *, double *, double *, double *,
                             double *, int);
     extern int transformDensity(actionInformation *, 
                                 double *, double *, double *, double *, int);
     extern int transformPairDist(actionInformation *, double *, double *, double *,
                                 double *, int);
     extern int transformImgDist(actionInformation *, double *, double *, double *,
                                 double *, int);
     extern int transformOrderParameter(actionInformation *, double *, double *, double *,
                                double *, int);
   
     extern actionInformation* ptrajCopyAction(actionInformation**);
   .
   .
       

2. The new commands have to be added to dispatch.c.

   Token ptrajTokenlist[] = {
   .
   .
     {"2drms",          5, -1, TRANSFORM_2DRMS,           ptrajSetup},
     {"mrt",            3, -1, TRANSFORM_MRT,             ptrajSetup},
     {"density",        4, -1, TRANSFORM_DENSITY,         ptrajSetup},
     {"order",          5, -1, TRANSFORM_ORDERPARAMETER,  ptrajSetup},
     {"pairdist",       5, -1, TRANSFORM_PAIRDIST,        ptrajSetup},
     {"imgdist",        4, -1, TRANSFORM_IMGDIST,         ptrajSetup},
     {"go",             2, -1, TRANSFORM_TRANSFORM,       ptrajSetup},
   .
   .
       

3. Also ptraj.c must be updated.

     switch ( type ) {
   .
   .
     case TRANSFORM_2DRMS:
   
       action->type = TRANSFORM_2DRMS;
       action->fxn  = (actionFunction) transform2dRMS;
       break;
   
     case TRANSFORM_MRT: /* new */
   
       action->type = TRANSFORM_MRT;
       action->fxn  = (actionFunction) transformMRT;
       break;
   
     case TRANSFORM_DENSITY: /* new */
   
       action->type = TRANSFORM_DENSITY;
       action->fxn  = (actionFunction) transformDensity;
       break;
   
     case TRANSFORM_ORDERPARAMETER: /* new */
   
       action->type = TRANSFORM_ORDERPARAMETER;
       action->fxn  = (actionFunction) transformOrderParameter;
       break;
   
     case TRANSFORM_PAIRDIST: /* new */
   
       action->type = TRANSFORM_PAIRDIST;
       action->fxn  = (actionFunction) transformPairDist;
       break;
   
     case TRANSFORM_IMGDIST: /* new */
   
       action->type = TRANSFORM_IMGDIST;
       action->fxn  = (actionFunction) transformImgDist;
       break;
   
     case TRANSFORM_TRANSFORM:
     case TRANSFORM_NOOP:
   .
   .
       

4. Finally, compile as usual.

Usage

MRT

Square brackets mean optional parameters. In the following defaults are given in parenthesis.

The reference point(s)/surface can be set in the following ways at the moment.

Diffusion

Square brackets mean optional parameters. In the following defaults are given in parenthesis. A simple Perl script is provided to compute window averages.

Density

The atom selections must be centered at the origin before calculating the density. See also example input file.

Square brackets mean optional parameters. In the following defaults are given in parenthesis.

Order Parameter

The order parameters S_x, S_y, S_z and |S_CD| are calculated. S_z is the vector joining carbons C_n-1 and C_n+1, S_x the vector normal to the C_n-1–C_n and C_n–C_n+1 plane and S_y is the third axis in the molecular coordinate system. The order parameter is then calculated from S_c = 0.5<3cos²θ> - 1, where θ is the angle to the chosen reference axis. See example input file.

Pair-Distance Distribution Function

Square brackets mean optional parameters. In the following defaults are given in parenthesis.

Distance to Images

Contact

References:

1. R. W. Impey, P. A. Madden and I. R. McDonald, J. Phys. Chem. 87(1983), 5071.
2. A. E. Garcia and L. Stiller, J. Comput. Chem. 14(1993), 1396.
3. C. Schröder, T. Rudas, S. Boresch, O. Steinhauser, J. Chem. Phys. 124(2006), 234907.