The GROMOS Interface
Command Line Arguments
Some of the arguments are directly used by the gromos
executable. Refer to the documentation of gromos for a detailed and
up-to-date explanation of them.
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords= |
Fragment tag
|
yes |
none |
Initial configuration of the system |
| executable= |
keyword |
no |
grforce.64 |
gromos executable |
| topology= |
file |
yes |
none |
The gromos topology file |
| npm= |
integer |
yes |
none |
The number of solute molecules |
| ntc= |
integer |
no |
1 |
GROMOS keyword (SHAKE)
1: no SHAKE is performed (solute)
2: SHAKE the bonds involving hydrogens (solute)
3: SHAKE all bonds (solute) |
| ntb= |
integer |
no |
0 |
GROMOS keyword concerning periodic boundary conditions (-2 ... 2):
<0: truncated octahedron periodic boundary conditions
>0: rectangular/monoclinic periodic boundary conditions
0: vacuum
abs(ntb)=2: the virial (pressure) is calculated
|
| box= |
Tcl List
|
no |
none |
Defines the bounding box, { x y z }. |
| debug= |
Boolean
|
no |
off |
Provide additional output quantities (off, on). |
| rcutp= |
real |
no |
0.8 |
Cut-off used in pairlist construction. |
| rcutl= |
real |
no |
1.4 |
Cut-off used in long range interaction. |
| epsrf= |
real |
no |
54.0 |
Epsilon used in reaction-field
calculation (0.0 or > 1.0). |
| appak= |
real |
no |
0.0 |
Kappa used in reaction-field calculation. |
| rcrf= |
real |
no |
1.4 |
Cut-off radius used in reaction-field calculation |
| ntg= |
integer |
no |
0 |
Controls free-energy calculation:
0: no perturbation is applied
1: calculate dV/dRLAM perturbation
2: calculate dV/dRMU perturbation
3: calculate both derivatives
Other values than 0 require specification
of pertfile. |
| rlam= |
real |
no |
0.0 |
Initial value for lambda in free-energy calculations. |
| pertfile= |
file |
no |
none |
Perturbation topology file. Mandatory if ntg
is not 0. |
| mm_defs= |
Tcl List
|
no |
none |
ignored |
| atom_attributes= |
Tcl List
|
no |
none |
ignored |
| atom_types= |
Tcl List
|
no |
none |
ignored |
| atom_charges= |
Tcl List
|
no |
none |
ignored |
| atom_pols= |
Tcl List
|
no |
none |
ignored |
| atom_names= |
Tcl List
|
no |
none |
ignored |
| delete_charges= |
Tcl List
|
no |
none |
ignored |
| export_charge_list= |
Tcl List
|
no |
none |
ignored |
Because it does not attempt to modify the topology generated (in
contrast to the dl_poly interface that creates the DL_POLY
topology) the GROMOS interface will ignore the following arguments
mm_defs atom_attributes atom_types atom_charges atom_pols
atom_names delete_charges export_charge_list. For compatability
these arguments are silently ignored.
|
