Control file format

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

PMFLib strictly checks that all parts of the control file were correctly understood in the context of the methods used. All keyword lines that were successfully read and used are marked as processed. If any line, including section or group declarations, remains unprocessed, the calculation cannot proceed and is terminated prematurely. The user must then examine the control file and fix all reported inconsistencies.

Keyword lines consist of at least two records. The first word is the key name. The remaining words define its value. Keys can be of several types, which are described here.

Example of a PMFLib input file

# driver setup, section [amber] is automatically added to the 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 information about PMF progress to the ABF trajectory
frestart        off

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

# monitor the 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