Lmanal

Usage:

lmanal [-O] -i lmdin -o lmdout -c inpcrd -l lmode


-O

Overwrite output files if they exist.

This program will compute time correlation functions from Langevin modes. Note that since the time-independent aspects of the molecular normal mode description are independent of solvent viscosity, all of the equal-time correlations (such as rms fluctuations in cartesian or internal coordinates) will be the same as for the vacuum calculation. Hence the companion program nmanal should be used to compute those.

Input description for the lmdin file:

namelist default meaning
&data
ntrun 1 'type of run' flag
1: correlation function calculated is
for the deviation of the length of
the vector from the reference value
in the minimum energy structure.
i.e., /
2: for the orientation of the vector
i.e.,
3: the frequency distribution is plotted
i.e., the imaginary parts of the
eigenvalues are counted at every interval
of 10 wavenumbers. Other input parameters
are irrelevant.
kup 1
lup 2 atom numbers defining a position vector
nvect 12 number of langevin modes to be used
tf 2.0 final time for correlation functions
i.e., t ranges from 0.0 to tf picoseconds
np 1000 number of points at which to calculate
correlation function between t = 0.0 and
t = tf ps.
bose .false. .true. if quantum (Bose) statistics are to be
used in populating the modes; =.false. (default)
if classical (Boltzmann) statistics are to be
used.
&end

The input file inpcrd is a standard Amber coordinate file; the file lmode is that created by the nmode program with ntrun = 5. Output files are CORF ( if ntrun = 1 or 2 ) and DENS, CUMU (if ntrun = 3.) All of the output files (except lmdout) are input files for the package, which will create plots of the correlation functions. You should(?) have little trouble converting them to some other plotting package in order to see the correlation functions.

+-----------------------------------------------------------------+
|	     Sample input file for nmode with ntrun=1		  |
+-----------------------------------------------------------------+
|								  |
| get vibrational modes for staph nuclease ternary complex	  |
| &data								  |
|     ntrun = 1,	  do vibrational calculation		  |
|     cut=10.0,		  cutoff; use same value in minimization  |
|     idiel=0,		  distance-dependent dielectric		  |
|     nvect=6753,	  write out all 3*N modes...		  |
|     ivform=0,		  ...in unformatted form...		  |
|     ilevel=0,		  ...with no removal of trans. & rotation |
|     drms = 0.0001,	  will complain if rms gradient is not	  |
|			      less than this			  |
| &end								  |
+-----------------------------------------------------------------+

+------------------------------------------------------------------+
|	     Sample input file for nmanal with ntrun=7		   |
+------------------------------------------------------------------+
|#								   |
| Get N-H S**2 values from quasi-harmonic modes			   |
| &data								   |
|  ntrun=7,		  compute dipole-dipole correlation fns.   |
|  nvect=4496,		  this many modes in input file		   |
|  ibeg=1, iend=4496,	  use all of the modes for the calculation |
|  ivform=0		  unformatted modes files		   |
|  natom=1529,		  molecule has this many atoms		   |
|  ihsful=0,		  do no include distance fluctuations	   |
| &end								   |
|3 4			  atom numbers for N and H of residue 1	   |
|11 12								   |
|20 21								   |
|28 29								   |
|38 39								   |
+------------------------------------------------------------------+