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

[Dallas Warren]

Thanks for the suggestion Chris.  Had a quick look and can't see easily how to do this, but I think I am at a point now where it is not an issue and don't have to actually do this.

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: Saturday, 2 November 2013 3:50 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Gibbs Energy Calculation and charges
> 
> Dear Dallas:
> 
> Seems like you could test Michael's idea by removing all 1-4 NB
> interactions from your topology. It won't produce any biologically
> useful results, but might be a worthwhile check to see if indeed this
> is the issue.
> 
> To do this, I figure you would set gen-pairs to "no" in the [ defaults
> ] directive of forcefield.itp, remove the [ pairtypes ] section from
> ffnonbonded.itp, and remove the [ pairs ] section from your molecular
> .itp file. (You can quickly check that the 1-4 energy is zero in all
> states to ensure that this works).
> 
> If that gives you the result that you expect, then you could go on to
> explicitely state the 1-4 interactions for the A and B states (I
> presume that this is possible). Of course, you should be able to jump
> directly to this second test, but the first test might be useful
> because it rules out the possibility that you make a typo somewhere.
> 
> Chris.
> 
> -- original message --
> 
> 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
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