Control file format

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Control files used by PMFLib are plain ASCII text files consisting from three type of entries: groups, sections, and keyword lines. Keyword lines can only be placed into sections, sections can only be placed into groups. If no group is specified then sections are placed into the {MAIN} implicit group. Empty lines are silently ignored. The setup can be commented. Comments begin with '#', '!', '*' characters, which can be placed anywhere on a line. If the leading comment character is not in the first column then it must be preceded by a white character.

PMFLib strictly controls if all parts of a file were understood correctly in the context of used methods. All keyword lines that were successfully read and used are marked as processed. If some line (including sections or groups) are left unprocessed the calculation cannot proceed and is prematurely terminated. An user has to examine control file and fix all inconsistencies found.

Keyword lines are composed at least from two records. The first word is name of key. The remaining words are its value. Keys might be of several types that are described here.

Example of PMFLib input

# driver setup, section [amber] is automatically added to implicit {MAIN} group
[amber]
... pmemd or sander setup is here ...

# PMFLib setup ----------------------------------------------------
{PMFLIB}

# adaptive biasing force (ABF) simulation is requested
[abf]
fmode           1
fsample         100  
ftrjsample      100   # write info about PMF progress to ABF trajectory
frestart        off

# together with multiple walkers approach
[abf-walker]
fserverkey      server.key

# we would also like to monitor progress of selected CVs 
[mon]
fmode           1
fsample         100

# specification of collective variables 
{CVS}
[DIS]
name             d1
group_a         :102,200,476,477,480 & @N,CA,C
group_b         :543

[DIS]
name            d2
group_a         :544
group_b         :555

# collective variables used in the ABF simulation 
{ABF}
[CV]
name            d1
min_value       15.25
max_value       32.75
nbins           35

! monitored collective variables 
{MON}
[CV]
name            d2