[gmx-users] g_lie

[David]

On Fri, 2004-02-13 at 23:25, Tivadar Orban wrote:
> Hi
> I am having problems making g_lie to work.
> What I did is:
> 1. ran a simulation of the ligand is solution
>    1.1 in mdp file I set
>    energygrps = ligand sol
>    grompp -n index.ndx having groups ligand and sol
>    1.2 g_energy and get the avarage of [Coul-SR Ligand-sol]
>    1.3 g_energy and get the avarage of [LJ Ligand-sol]
OK so far

>    1.4 ran g_lie -f ener.edr -Elj avarage_[LJ Ligand-sol] -Eqq [Coul-SR
> Ligand-sol]
> 
this step not necessary

> 2. ran a simulation of ligand+enzyme in solution
>    1.1 in mdp file I set
>    energygrps = ligand enzyme
you need a group sol as well

>    grompp -n index.ndx having groups ligand and enzyme
>    1.2 g_energy and get the avarage of [Coul-SR Ligand-Enzyme]
>    1.3 g_energy and get the avarage of [LJ Ligand-Enzyme]
these two steps not necessary

>    1.4 ran g_lie -f ener.edr -Elj avarageg_lie -f ener.edr -Elj avarage_[LJ Ligand-Enzyme] -Eqq
> avarage_[Coul-SR Ligand-Enzyme]
> 
here you run 
g_lie -f ener.edr -Elj avarage_lie  -Eqq avarage_[Coul-SR Ligand-SOL]
-ligand ligandname

where the values come from the ligand/solvent simulation.

> 

> I think that I am doing something wrong because g_lie gives me the following
> output
> (i.e. there are no energy terms for LJ and Coul.  DGbind has nan units):
> 
> Opened ener.edr as double precision energy file
> Using the following energy terms:
> LJ:
> Coul:
> 
> Back Off! I just backed up lie.xvg to ./#lie.xvg.1#
> Last frame read 1000
> DGbind = 463.709 (nan)
> 
> Any idea what the problem is?
> 
> Regards,
> Tivadar, Orban
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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