On 6/8/14, 4:41 PM, Albert wrote:
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......
Well, -Elj and -Eqq are necessary. You've left them both at zero. Do you know
the proper protocol for the energy terms that need to be saved and the
post-processing necessary to run a LIE calculation? If not, check the archive;
this question comes up frequently.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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