brimin

brimin is a program to efficiently carry out energy minimization.

Click here for download and installation instructions.

The program is invoked as follows:

brimin -inpcrd inpcrd -prmtop prmtop -amb2syb amb2syb -settings settings_file -mincrd min.crd

For example,

prompt% brimin -inpcrd alabeta.inpcrd -prmtop alabeta.prmtop -amb2syb amb2syb.txt -settings settings_amber.txt -mincrd alabeta_min.crd

The inpcrd and prmtop files are generated using the tleap or xleap utility of AMBER.
The amb2syb.txt file comes from the 'tables' subdirectory of the sietraj package.
A sample settings file is shown below.

CUTOFF 8.0
DIELEC_FUNC DISTANCE_DIE
DIELEC_CONST 4.0
GRMSTOL 0.001
MAXFCALLS 10000
RESTRAIN_NONH 4.0
# Lessen output info
SILENT

GRMSTOL is the convergence tolerance for the rms gradient.

The screen output generated by the above settings and the alabeta input files is

Loaded Britcl-v2.2b.so
Britcl_functions.tcl,v 1.10 2008/08/04
Reading prmtop ...

Reading inpcrd ...

Constructing 1-5 array ...

Setting up conjgrad ...

Calc initial energy ...

energies:
BOND: 0.570447
ANGLE: 2.022497
ITOR: 0.000000
TOR: 23.258763
1-4 vdw: 8.412192 1-4 elec: 16.119312
1-5 vdw in: -2.666702 1-5 elec in: -17.794005
1-5 vdw out: -0.057929 1-5 elec out: -0.035116

total: 29.829459

2 nonbonded list updates

energies:
BOND: 0.436878
ANGLE: 0.933845
ITOR: 0.000000
TOR: 20.633374
1-4 vdw: 6.610308 1-4 elec: 15.563507
1-5 vdw in: -4.632009 1-5 elec in: -17.474503
1-5 vdw out: -0.049890 1-5 elec out: -0.093513

total: 21.927998

The following illustrates how to define an atom set that can be subsequently used as the hotset in a local energy minimization. Ranges of atom ids separated by commas have to be supplied.

# Add these lines to your settings file to define a hotset.
DEFINESET MYSET 1-7,10-15
# You can then use this set in the following line.
HOTSET MYSET

Add the line
HOTSET setname
if only a set of atoms are allowed to move during minimization. When a HOTSET is defined, the reported energies only include those for the mobile atoms.

Send feedback, suggestions or queries to mm-admin@nrc-cnrc.gc.ca.