bilayer chain tilt - 07/13/05 01:10 AM

The following script uses a vector from C3 to C13 of each lipid chain to estimate the overall chain tilt.

* DPPC 80 lipid gel; chain tilt time series

*

bomblev -2

! READ RTF, PARAM, PSF, AND COOR FILES

stream rtfprm.str

stream psfcrd.str

! COMPUTE TIME SERIES LIMITS; 1 NS SAVED AT 1 PS INCR IN EACH FILE

calc mxt = 1000 * @N

! FOUR VECTORS PER LIPID + TEN MORE

calc mxs = 10 + ( 4 * 80 )

correl maxt @MXT maxs @MXS maxa ?NATOM noupdate

! DECLARE ACCUMULATION SERIES (FOR AVGS) FIRST

enter aav zero

enter bav zero

! LOOP OVER LIPIDS; DEFINE VECTOR LENGTH (R) AND Z COMPONENT

set k 1

label elp

enter r@K vect r L @K C23 L @K C213 ! BETA CHAIN

enter s@K vect r L @K C33 L @K C313 ! GAMMA CHAIN

enter z@K vect z L @K C23 L @K C213

enter w@K vect z L @K C33 L @K C313

incr k by 1

if k le 80 goto elp

! OPEN FILES (COPIED TO /scratch FOR EFFICIENCY)

set j 1

label olp

calc u = 7 + @J

open unit @U file name /scratch/dyn@J.trj

incr j by 1

if j le @N goto olp

traj first 8 nunit @N

set k 1

label tlp

! NORMALIZE Z COMPONENT (DIVIDE BY R)

mantim z@K ratio r@K

mantim w@K ratio s@K

! IGNORE SIGN; NEEDED TO AVG OVER BOTH LEAFLETS

mantim z@K abs

mantim w@K abs

! SUM OVER CHAINS, EACH SEPARATELY

mantim aav add z@K

mantim bav add w@K

incr k by 1

if k le 80 goto tlp

! DIVIDE BY N; RESULT IS AVG Z PROJECTION, WHICH IS COS(THETA)

mantim aav divi 80.

mantim bav divi 80.

! CONVERT COS TO AN ANGLE

mantim aav acos

mantim bav acos

! OUTPUT FILE WITH (TIME, BETA-TILT, GAMMA-TILT) FOR EACH TIME POINT

edit aav veccod 2

open unit 2 write card name tiltavg.dat

write aav unit 2 dumb time

* dummy

*

end

stop