This computation is made by
bileldens utility. It is supposed
that a membrane-like system is oriented in XY-plane. The utility computes
the electron density, the mass density, the charge density, and the
electrostatic potential across membrane in Z-direction.
f77 -O3 -o bileldens bileldens.f tranal_base.f
Input parameters for this utility follow after the trajectory parameters
in the NAMELIST block
$ELDEN parameter=value(s), ... $END
The following parameters are used:
FDENS = <filename>
Defines name of the output file
IRT = <int.num>
Defines the type number of ``lipid'' molecules. The middle plane of the bilayer is calculated from the center-of-mass Z-coordinate of molecules of this type. Eventually the molecules are transfered across the periodic boundaries to keep the whole bilayer within the same periodic cell.
NA = <int.num>
Defines the number of ``bins'' for computation of densities
ZMAX = <value>
Defines the borders of the interval in Z-direction. The densities and the electrostatic potential are calculated in the range of : relative to the membrane middle plane
IATE = <list of values>
This optional parameter defines which sites to take into account while calculating the densities. Default is all sites. A value equal to 1 says that the given site is accounted while 0 says that this site is not accounted. For example, if the system consists of DMPC lipids (118 atoms in molecule), water (3 atoms), Na and Cl ions, this compute contributions from the lipids only:
IATE = 118*1,5*0
while this compute contribution from the water oxygen only:
IATE = 118*0,1,0,0,0,0
LCHG = <logical>This parameter tells whether to use a special file containing charges for computation of electron density. In case
LCHG = .true., a file defined by parameter
FCHGis read; it determines contribution of each site into the electron density. If
LCHG = .false., contribution of each site is defined from the first letter of the site name (for and atoms only) and corrected by the partial atom charges.
FCHG = <file_name>
File name for the case
LCHG = .true.
LSYM = <logical>
This parameter tells whether to symmetrize the computed densities relative to the membrane middle plane. Note that even slightest asymmetry in the charge distribution may lead to a potential difference from the both sides of membrane.