# [gmx-users] g_lie and PME

Wed May 11 17:27:32 CEST 2005

```Hi,

after carefully reading all the threads on this topic, I got stuck at the
same point.

Just to clarify the procedure for a NEUTRAL ligand, where I did both
simulations (Protein/LIG/SOL and LIG/SOL).

Eqq = Coul-SR(LIG-SOL) + Coul-LR(LIG-SOL) + Coul-14(LIG-SOL)
Elj = LJ-SR(LIG-SOL) + LJ-LR(LIG-SOL) + LJ-14(LIG-SOL)

with all values from the LIG/SOL simulation. Is this correct?

When I now have a CHARGED ligand, I follow the mentioned procedure (1.
tpbconv -zeroq; 2. mdrun -rerun traj.trr) to get a correct value for the
Coulomb energy.
Taking a look on Coul-SR(LIG-SOL, rerun), Coul-LR(LIG-SOL, rerun),
Coul-14(LIG-SOL, rerun) shows, that they are all zero. So which energy
terms do you use to calculate the difference (=Eqq)? And how big is
normally the difference between uncorrected and corrected Eqq?

Jens

Anton Feenstra wrote:

> Lei Zhou wrote:
>
> > Hi,
> >
> > I am trying to calculate the binding free energy of a ligand to a
> > protein, using g_lie based on two simulations (ligand in h2o and
> > ligand with protein). Someone mentioned that LIE is originally
> > developed with cutoffs, thus it is not necessary to put long range
> > energies (both coul and LJ) into consideration? And also what is the
> > most convenient way to calculate the long range Coul energy beteen
> > ligand and h2o, if necessary?
>
> Simulate ligand in h2o, extract energies. 'Re-run' with charges for
> ligand set to zero (iirc, there is an option in tpbconv to 'tweak'
> charges to zero for some group of atoms), and extract those energies.
> The difference between both sets is the ligand-water coulomb
> interaction. Possibly, due to numerical precision, you may need to use
> '-rerun' energies in both cases.
>

>
> > Is there a standard protocal for doing mdrun -rerun? Some people
> > suggested the following:
> > nslist=1; constaints=none; nstenergy=1. Are these setting necessary?
>
> No, -rerun will force neigbourlist update for each frame read.
> Constraints may be re-enforced but that should not change your (already
> constrained) trajectory coordinates. nstenergy may be a good idea, I
> don't know right away if by default -rerun forces writing energies out
> for each trajectory frame.
>
> In general, simply 'mdrun -rerun' would most often work.
>
> --
> Groetjes,
>
> Anton
>
> * NOTE: New Phone & Fax numbers (below) *
>
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
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> | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
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--
========================================================
Jens Krüger