[gmx-users] g_lie and PME
mercutio at uni-paderborn.de
Wed May 11 17:27:32 CEST 2005
after carefully reading all the threads on this topic, I got stuck at the
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
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?
Thanks for your help,
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.
> * NOTE: New Phone & Fax numbers (below) *
> _____________ _______________________________________________________
> | | |
> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610 |
> | | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
> | | "If You See Me Getting High, Knock Me Down" (RHCP) |
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
mercutio at uni-paderborn.de
Warburger Str. 100 * 33098 Paderborn * Tel.:05251-602183
Ellersteg 3 * 33100 Paderborn-Dahl * Tel.:0176-20042288
More information about the gromacs.org_gmx-users