MRT | Diffusion | Density | Order Parameter | Pair-Distance Distribution Function | Distance to Images
MRT (ptraj only)
| mrt | out <filename>[autocorr <filename>tcorr <time>toffset <time>] |
| [lower <dist>] [upper <dist>] [time <t>] [tstar <t>] [noimage] | |
| [solvent <mask>| solute <mask>] (siteatoms <mask>| [onemol] <sitemask>| | |
| <sitemask1> ... <sitemaskN>) |
Square brackets mean optional parameters. In the following defaults are given in parenthesis.
| out | Output file: time vs. MRT correlation function for each mask. |
| autocorr | Optional autocorrelation code. (off) |
| tcorr | (autocorr) Maximum correlation time = size of windows in ps. (400.0 ps) |
| toffset | (autocorr) Time step/gap between windows (code computes parallel windows to improve statistics). (10.0 ps) |
| solvent | Optional solvent mask which overrides the internal definition of solvent. May also be changed with the solvent command (see ptraj manual). The centre of mass is used as the reference point. |
| solute | Optional mask representing a single site (centre of mass). If this is used solvent (see above) is ignored. |
| lower | Smaller distance from reference point(s). (0.01 Å) |
| upper | Larger distance from reference point(s). (3.5 Å) |
| time | Time step in the trajectory. (1.0 ps) |
| tstar | t* to account for short term excursions (see Impey paper[1]). (0.0 ps) |
The reference point(s)/surface can be set in the following ways at the moment.
| siteatoms <mask> | Atoms in the mask will be considered as individual reference points, i.e. if the mask expands to 100 atoms then 100 MRTs will be computed, useful for "quick scanning" of many sites. |
| onemole <sitemask> | All atoms in the mask constitute a single reference site, i.e. if the mask contains all atoms of a protein then a single MRT around that protein will be calculated. IMPORTANT: may be very slow!!! |
| <sitemask1>... | After all named parameters have been processed each remaining parameter will be interpreted as a single reference site. If it contains several atoms the centre of mass will be taken as reference point. |
Diffusion
| diffusion | mask <mask>[out <file>] [time <time per frame>] |
| [mask2 <mask> lower <distance> upper <distance> nwout <file>] | |
| [avout <file>] [x|y|z|xy|xz|yz|xyz] [distances] [com] |
Square brackets mean optional parameters. In the following defaults are given in parenthesis.
| mask | Atoms for which MSDs will be computed. |
| out | Output file: time vs. MSD. |
| time | Time step in the trajectory. (1.0 ps) |
| mask2 | Compute MSDs only within the lower and upper limit of mask2. IMPORTANT: may be very slow!!! |
| lower | Smaller distance from reference point(s). (0.01 Å) |
| upper | Larger distance from reference point(s). (3.5 Å) |
| nwout | Output file containing number of water molecules in the chosen region, see mask2. (off) |
| avout | Output file containing average distances. (off) |
| x|y|z|xy|xz|yz|xyz | Computation of the mean square displacement in the chosen dimension. (xyz) |
| distances | Dump un-imaged distances. By default only averages are output. (off) |
| com | Calculate MSD for centre of mass. (off) |
Density
The atom selections must be centred at the origin before calculating the density.
| density | out <filename> [delta <resolution>] [x|y|z] |
| [number|mass|charge|electron] [efile <filename>] <mask1> ... <maskN> |
Square brackets mean optional parameters. In the following defaults are given in parenthesis.
| out | Output file for histogram: relative distances vs. densities for each mask. |
| delta | Resolution, i.e. determines number of slices. (0.25 Å) |
| x|y|z | Coordinate for density calculation. (z) |
| number|mass|charge|electron | Number, mass, partial charge (q) or electron (Ne - q) density. To convert the electron density to e-/Å3 divide by the (average) area spanned by the other two dimensions. (number) |
| efile | Optional file with electron numbers Ne for each atom type. If this file is not supplied the command assumes that atom types starting with 'H', 'C', 'N', 'O', 'P' and 'S' are the actual elements. The format of the file is as follows. Comments are lines starting with '#' or empty lines. All other lines must contain the atom type followed by an integer number for the electron number. Entries must be separated by spaces or '='. |
| mask1 ... maskN | Arbitrary number of masks for atom selection, the output will contain a column for each mask. |
Order Parameter
The order parameters Sx, Sy, Sz and |SCD| are calculated. Sz is the vector joining carbons Cn-1 and Cn+1, Sx the vector normal to the Cn-1-Cn and Cn-Cn+1 plane and Sy is the third axis in the molecular coordinate system. The order parameter is then calculated from Sc = 0.5<3cos2θ> - 1, where θ is the angle to the chosen reference axis.
| order | out <filename> [x|y|z] [unsat <mask>] | [taildist <filename> [delta <resolution>] tailstart <mask> tailend <mask>] | <mask0> ... <maskN> |
| out | Output file for order parameters: Sx, Sy, Sz (each succeeded by the standard deviation), and two estimates for the deuterium-order parameter |SCD| = 0.5Sz and |SCD| = -(2Sx + Sy)/3. If scd is set then the order parameter directly computed from the C-H vectors is output. |
| x|y|z | Reference axis. (z) |
| unsat | Mask for unsaturated bonds. Sz is calculated for vector Cn-Cn+1. This is only relevant if scd (below) is not set, i.e. order parameters are calculated from carbon position only. |
| scd | Calculate the deuterium-order parameter |SCD| directly from the C-H vectors (masks must contain C-H-H triplets, see below). Otherwise the order parameter is estimated from carbon positions only (masks must contain only relevant carbons). (false) |
| taildist | Optional output file for end-to-end distances. |
| delta | Optional resolution for taildist. (0.1) |
| tailstart | Mask for the start of the tail. Must be given if taildist. |
| tailend | Mask for the end of the tail. Must be given if taildist. |
| mask0 ... maskN | Masks for each group in the lipid chain. Carbons must be given in bonding order. If scd the masks must be made up of C-H-H triples, hence hydrogens to double bonds must be enumerated twice while methyl groups require an additional mask which will also create two entries in the output. |
Pair-Distance Distribution Function
| pairdist | out <filename> mask <mask> [delta <resolution>] |
Square brackets mean optional parameters. In the following defaults are given in parenthesis.
| out | Output file for histogram: distance, P(r), s(P(r)). |
| mask | Atoms for which distances should be computed. |
| delta | Resolution. (0.1 Å) |
Distance to Images (ptraj only)
| imgdist | out <filename> mask <mask> threshold <distance> |
| out | Output file listing distances shorter than the threshold. |
| mask | Atoms for which distances should be computed. |
| threshold | Report all distances smaller than this value. |
Contact
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