[gmx-users] Structuring as function of z - gmx order
Dallas.Warren at monash.edu
Tue Sep 2 06:02:49 CEST 2014
Just worked out why h2order is not working, since it is dealing with the dipole moment, using atoms in that which are zero charge is going to give zeros.
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> Dallas Warren
> Sent: Tuesday, 2 September 2014 12:00 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Structuring as function of z - gmx order
> I have a system that contains a constrained crystal molecules plus free
> molecules and water. What I would like to obtain is a measure of the
> structuring of the free molecules as a function of the z direction
> across the box.
> Using GROMACS 5.0
> First attempt I tried using gmx h2order, however appears that unless
> atom names are oxygen/hydrogen it does not generate the data. Works
> fine for the water in the system, but when go to non-water, output is
> zeros only.
> Next tried using gmx order. I can get it to generate the order
> parameter (S) with respect to the z axis as a function of the z
> distance fine (using -os -sl 100), as well as x axis-x direction and y
> axis-y direction (using -d x and -d y).
> However, what I would like is to have the values for Sx, Sy and Sz as a
> function of distance across the box in the z direction (i.e. within
> slices taken across the x-y plane). Sz can get fine, and that does
> tell me something about the ordering of the molecules. However, since
> that is only relative to one axis, that is not the entire story.
> Using -noszonly with -os generates the Sx, Sy, Sz values; but only in
> the -o output file (overall/average value?), the -os file is not
> Using -szonly will generate the order parameter per slice in the
> direction specified by -d, as noted above.
> Should the script be generating the order parameter relative to all
> three axis along a particular axis direction when -noszonly is
> Or is there an alternative scrip that someone could suggest to use?
> Thank you for any suggestions and input.
> Catch ya,
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
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