Input/Output files

Input files:

*Main input

specifying parameters of the Monte-Carlo sampling, inverse solver and input/output files: magic.inp

*Topology

for every CG-molecular type: [MCM]*.mcm

*Reference distribution functions

: [RDFnPOT]*.rdf

Starting trial potentials

[RDFnPOT]*.pot. If not provided (or partially provided), the missing trial potential will be deduced from the RDF-file as potential of mean force or zero-potential, depending on the user's choice.

Initial geometry for MC-process

in [XMOL]*.xmol or *.xtc (optional). User can provide individual file for every parallel process:
name-of-the-system.p<process-number>.i<iteration-number>.start.xmol
or just a single file with multiple frames, which will be randomly read by all processes.

Exclusion-files:

(optional) [exclusions.dat]*.dat Files with non-bonded exclusions specification, one for short-range interactions and another for the electrostatics. If not provided, default exclusions will be used: atoms bonded by pairwise or angle bond will be excluded from both short-range and electrostatic interactions.

External Trajectory:

(optional) *.xtc or *.xmol . External trajectory (generated by external MD software) can be used instead of Monte-Carlo sampling, then MagicCore will only update the potentials.

Cross Correlation Matrix

(optional) - binary file storing cross-correlation matrix. If it is provided, MagicCore will read the matrix, update it with new values sampled in the current MC-run, and write back the updated matrix to the file. This is useful when you want to split a long simulation into several shorter pieces. NB! The file can become rather large for system with multiple interactions.

Output files:

General output

By default it is printed on the screen, but it is recommended to redirect it to a file (see example below)

Log/journal for every parallel process

. name-of-the-system.p<process-number>. In serial run it is written to the general output.

Resulting effective potentials

(starting potential for current iteration + correction): name-of-the-system.i<iteration-number>.pot

Monte-Carlo trajectory

of each parallel process:
name-of-the-system.p<process-number>.xmol

The final snapshot

of the system of each parallel process and iteration:
name-of-the-system.i<iteration-number>.p<process-number>.start.xmol This file can be used as a starting configuration for a next consequent series of MC runs. In case of a parallel MC run, a set of files is produced which are used as starting configurations for each processors at the next iteration.

Cross Correlation Matrix

Binary file storing cross-correlation matrix, see above.

Execution:

serial execution:

magic magic.inp > magic.out

parallel execution:

mpirun -np n_of_proc magic magic.inp > magic.out