[gmx-users] why deltaG=0?

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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