[gmx-users] g_lie and PME
zhoumadison at gmail.com
Fri May 13 04:34:48 CEST 2005
Hi, thank you for the reply. I still have the following questions
about g_lie and PME:
1, to calculate the Coul (or LJ ) energy between SOL and ligand,
should I include Coul-14 (or LJ-14) of ligand?
2, I did the mdrun -rerun as you suggested and got a Coul-LR value of
ligand-H2O about -250 kcal/mol (Coul-SR is about -200 kcal/mol). The
ligand coutains about 30 atoms and have one charge. Are those values
3. Coul-LR between ligand and SOL is calculated by re-run the original
trajectory files several times. But how is the Coul-LR between protein
and ligand handled by g_lie?
Thank you in advance.
On 5/10/05, Anton Feenstra <feenstra at few.vu.nl> 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.
> * NOTE: New Phone & Fax numbers (below) *
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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