[gmx-users] g_lie and PME

[Anton Feenstra]

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

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|  _   _  ___,| K. Anton Feenstra                                     |
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