[gmx-users] g_hyrorder

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 16 15:59:47 CET 2016

On 16/02/16 15:13, xy21hb wrote:
> Dear all,
> I wonder the which number I should give to feed the -sgang1 and -sgang2 if I calculate the water tetrahedral order in a simple lipid bilayer system.
> I searched extensively and read the source code hydorder.c but still have no idea in this case.
> However, Phi(i,j) in Eqn(3) of Chau and Hardwick 1998 Mol. Phys. paper seems okay to me.
> Best regards,
> Yao
You should provide the expected order parameter for the two phases in 
your system such that the program can find the phase boundary. For 
instance for ice you should expect 0. However I doubt that this program 
will give you any useful information, since it is mainly intended for 
water phases.
Read more in our paper:
http://dx.doi.org/10.1021/ct500459x | J. Chem. Theory Comput. 2014, 10, 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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