Hi Justin:
thx for reply. I use command g_lie -h to get the options and it
indicated as following:
Option Filename Type Description
------------------------------------------------------------
-f ener.edr Input Energy file
-o lie.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-Elj real 0 Lennard-Jones interaction between ligand and
solvent
-Eqq real 0 Coulomb interaction between ligand and solvent
-Clj real 0.181 Factor in the LIE equation for Lennard-Jones
component of energy
-Cqq real 0.5 Factor in the LIE equation for Coulomb component
of energy
-ligand string none Name of the ligand in the energy file
Which options do you think it would be necessary to be added for
calculation. For me I don't see I missed something important......
thx
Albert
On 06/08/2014 05:40 PM, Justin Lemkul wrote:
Probably a combination of things, including not saving the right
energy groups and missing several important command-line options.
-Justin
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