GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
GMX-HYDORDER(1) GROMACS GMX-HYDORDER(1)

gmx-hydorder - Compute tetrahedrality parameters around a given atom

gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
             [-o [<.xpm> [...]]] [-or [<.out> [...]]]
             [-Spect [<.out> [...]]] [-b <time>] [-e <time>]
             [-dt <time>] [-[no]w] [-d <enum>] [-bw <real>]
             [-sgang1 <real>] [-sgang2 <real>] [-tblock <int>]
             [-nlevel <int>]


gmx hydorder computes the tetrahedrality order parameters around a given atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details.

gmx hydorder calculates the order parameter in a 3d-mesh in the box, and with 2 phases in the box gives the user the option to define a 2D interface in time separating the faces by specifying parameters -sgang1 and -sgang2 (it is important to select these judiciously).

Options to specify input files:
-f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-n [<.ndx>] (index.ndx)
Index file
-s [<.tpr>] (topol.tpr)
Portable xdr run input file

Options to specify output files:

-o [<.xpm> […]] (intf.xpm)
X PixMap compatible matrix file
-or [<.out> […]] (raw.out) (Optional)
Generic output file
-Spect [<.out> […]] (intfspect.out) (Optional)
Generic output file

Other options:

-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-d <enum> (z)
Direction of the normal on the membrane: z, x, y
-bw <real> (1)
Binwidth of box mesh
-sgang1 <real> (1)
tetrahedral angle parameter in Phase 1 (bulk)
-sgang2 <real> (1)
tetrahedral angle parameter in Phase 2 (bulk)
-tblock <int> (1)
Number of frames in one time-block average
-nlevel <int> (100)
Number of Height levels in 2D - XPixMaps

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

2022, GROMACS development team
January 14, 2022 2021.5

Search for    or go to Top of page |  Section 1 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.