[gmx-users] RE: Gibbs Energy Calculation and charges

Michael Shirts mrshirts at gmail.com
Wed Oct 30 05:48:43 CET 2013 

I think the grammar got a little garbled there, so I'm not sure quite
what you are claiming.

One important thing to remember; 1-4 interactions are treated as
bonded interactions right now FOR COUPLE intramol (not for lambda
dependence of the potential energy function), so whether
couple-intramol is set to yes or no does not affect these interactions
at all.  It only affects the nonbondeds with distances greater than
1-5.  At least to me, this is nonintuitive (and we're coming up with a
better scheme for 5.0), but might that explain what you are getting?

On Tue, Oct 29, 2013 at 9:44 PM, Dallas Warren <Dallas.Warren at monash.edu> wrote:
> Just want this to make another pass, just in case those in the know missed it.
>
> Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0.
>
> Should that be the case?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> bounces at gromacs.org] On Behalf Of Dallas Warren
>> Sent: Tuesday, 22 October 2013 2:49 PM
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] RE: Gibbs Energy Calculation and charges
>>
>> I have completed the simulations using couple-intramol = yes
>>
>> Reminder, have a molecule that are calculating the Gibbs energy of
>> hydration and solvation (octanol).  In one topology the only difference
>> is the atomic charges have been doubled.  Considering that charges are
>> scaled linearly with lambda, the normal charge values of dH/dl from
>> lambda 0 to 1 obtained should reproduce that of the double charged
>> molecule from lambda 0.5 to 1.0.
>>
>> Here is the mdout.mdp file from one of the simulations using couple-
>> intramol = yes.  The difference with the simulations run using couple-
>> intramol = no is only that setting, checked using the diff command.
>> Copy of the mdout.mdp file can be found:
>>
>> http://ozreef.org/stuff/gromacs/mdout.mdp
>>
>> Changing to couple-intrmol = yes makes things significantly worse.
>>
>> Here are the plots of dH/dl obtained as a function of the charge of one
>> of the atoms, OE (calculated based on fact that at lambda = 0 fully
>> charged, lambda = 1 no charged)
>>
>> http://ozreef.org/stuff/gromacs/couple-intramol.png
>>
>> Anyone with some insight on what is going on here?
>>
>> >From the manual:
>> ________________________
>> couple-intramol:
>>
>>     no
>>         All intra-molecular non-bonded interactions for moleculetype
>> couple-moltype are replaced by exclusions and explicit pair
>> interactions. In this manner the decoupled state of the molecule
>> corresponds to the proper vacuum state without periodicity effects.
>>     yes
>>         The intra-molecular Van der Waals and Coulomb interactions are
>> also turned on/off. This can be useful for partitioning free-energies
>> of relatively large molecules, where the intra-molecular non-bonded
>> interactions might lead to kinetically trapped vacuum conformations.
>> The 1-4 pair interactions are not turned off.
>> ________________________
>>
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3052
>> dallas.warren at monash.edu
>> +61 3 9903 9304
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to
>> resemble a nail.
>>
>>
>> > -----Original Message-----
>> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> > bounces at gromacs.org] On Behalf Of Dallas Warren
>> > Sent: Thursday, 17 October 2013 3:32 PM
>> > To: Discussion list for GROMACS users
>> > Subject: [gmx-users] RE: Gibbs Energy Calculation and charges
>> >
>> > Chris,
>> >
>> > Thank you, that appears to be the issue then.
>> >
>> > Running them again now with couple-intramol = yes
>> >
>> > Will report back once that is completed with the results.
>> >
>> > Catch ya,
>> >
>> > Dr. Dallas Warren
>> > Drug Delivery, Disposition and Dynamics
>> > Monash Institute of Pharmaceutical Sciences, Monash University
>> > 381 Royal Parade, Parkville VIC 3052
>> > dallas.warren at monash.edu
>> > +61 3 9903 9304
>> > ---------------------------------
>> > When the only tool you own is a hammer, every problem begins to
>> > resemble a nail.
>> >
>> >
>> > > -----Original Message-----
>> > > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> > > bounces at gromacs.org] On Behalf Of Christopher Neale
>> > > Sent: Thursday, 17 October 2013 2:15 PM
>> > > To: gmx-users at gromacs.org
>> > > Subject: [gmx-users] Gibbs Energy Calculation and charges
>> > >
>> > > Ah, I see. I guess that you are using couple-intramol = no (the
>> > default
>> > > in v4.6.3 at least). That means
>> > > that the intramolecular charge-charge interactions are always at
>> > full-
>> > > strength (and therefore different).
>> > >
>> > > I would expect that normal at lambda=0 should be the same as double
>> > at
>> > > lambda=0.5 only for
>> > > couple-intramol = yes
>> > >
>> > > If you were using couple-intramol = yes already, then I am as
>> > confused
>> > > as you are.
>> > >
>> > > Chris.
>> > >
>> > > -- original message --
>> > >
>> > > You are correct in the first part of your statement, part that
>> isn't
>> > > correct is I expect for the same charge on the atom I expect it to
>> > give
>> > > the same dH/dl value.
>> > >
>> > > For example, for the OE atom that I provided the graphs for (
>> > > http://ozreef.org/stuff/octanol.gif and
>> > > http://ozreef.org/stuff/water.gif )
>> > >
>> > > Lambda       Normal
>> > > 0.0000    -0.5310
>> > >              Double
>> > > 0.0000    -1.0620
>> > > 0.5000      -0.5310
>> > >
>> > > Therefore, the normal charge molecule when lambda = 0 should be
>> > > identical to that double charge one when lambda = 0.5.  They should
>> > be
>> > > the same in all manners, LJ, bonds, charges etc.
>> > >
>> > > So would I not expect to get the same dH/dl value out?
>> > >
>> > > Catch ya,
>> > > --
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