[gmx-users] (no subject)

[gmx-users-admin at gromacs.org]

On Wed, 2002-10-23 at 17:44, David L. Bostick wrote:
> 
> Hello all,
> 
> I am interested in using David van der Spoel's method for calculating the
> total coulomb energy of a single ion with the rest of the system.  I just
> want to ask a few questions so I can feel comfortable with what I'm doing.
> 
> 1)If I take the original .edr file from the simulation, is the total
> coulomb energy of the system Coulomb (SR) + Coulomb (LR) as extracted by
> g_energy?  That is.. Coulomb 1-4 doesn't really factor in does it?
In this case it is constant, yes.

> 
> 2)Then if I set the ion charge to zero and rerun to generate a new .edr
> file and calculate the total coulomb energy again as Coulomb (SR) + Coulomb
> (LR), this will be the total PME energy for System_&_!ion-System_&_!ion?
Coulomb (SR) you can do in groups anyway, so you can get that more
accurate from the original run.
 
> 3)Then I can subtract the result of #2 from the result of #1 and obtain the
> total coulomb PME energy of System_&_!ion-ion?  Since there is only one
> ion, the coulomb energy of ion-ion is zero so I don't have to worry about
> it.
E(lr) = E(lr) (ion-ion) + E(lr) (ion-rest) + E(lr) (rest-rest)
Setting the ion charge to zero will give you E(lr) (rest-rest)
setting the rest to zero will give you E(lr) (ion-ion)
but if you have only one ion that term will be zero. Do check the charge
correction to PME, as that may be different when the total charge
changes.

> 4)If I write the total ewald sum in the traditional way,
> 
>       E = E(real) + E(reciprocal) + E(self) + E(dipole_correction)
> 
>   is the coulomb energy as extracted by g_energy as follows:
> 
>    Coulomb (SR) = E(real)
> 
>   and
> 
>    Coulomb (LR) = E(reciprocal) + E(self) + E(dipole_correction) ?
> 
>    How exactly are these terms divided among the two quantities Coulomb(SR)
>    and Coulomb(LR)?
Coulomb(LR) = E(reciprocal) + E(self) + E(dipole_correction)
Coulomb(SR) = E(real) 
 

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.