Re: [gmx-users] soft-core and coulomb transformation

[bharat v. adkar]

hi,
even i am also checking the ethane->methane case with the fix you 
suggested. equilibration values appear to be okay. will let you know by 
tommorrow the final results..

thanks

bharat


On Wed, 14 Nov 2007, Berk Hess wrote:

Hi,

The bug was indeed was I expected.
I have fixed it for version 3.3.3.

You might not notice it easily, since the direct space contribution is 
usually
larger than the mesh part.
But for a two particle system I got nan's.

Berk.


From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Subject: Re: [gmx-users] soft-core and coulomb transformation
Date: Mon, 12 Nov 2007 16:17:36 -0800

Berk,

>  But what do you mean with charging and discharging?
> 
>  Going one way or the other in lambda does not matter.
>  What matters is if there are particles that have zero charge
>  in the A-state topology, while they have a non-zero charge
>  in the B-state topology.

Sorry, what I mean by "charging" versus "discharging" is that
"charging" is where the A state has zero charges and the B state has
normal charges, and discharging is the reverse. So "charging" is the
scenario you describe, and "discharging" is the reverse.

David

>  Berk.
> 
> 
> > From: "David Mobley" <[EMAIL PROTECTED]>
> > Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > To: "bharat v. adkar" <[EMAIL PROTECTED]>
> > CC: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > Subject: Re: [gmx-users] soft-core and coulomb transformation
> > Date: Mon, 12 Nov 2007 10:26:37 -0800
> > 
> > Following up on this issue, discharging phenol in water appears to
> > give the same results as charging phenol in water. In other words, so
> > far the only cases for which there seem to be a problem are relative
> > calculations (and so far I haven't looked at this for any other than
> > Bharat's test cases).
> > 
> > Bharat, be sure you submit a bugzilla and we'll see how things go from
> > there. I may at some point try setting up some of my own relative free
> > energy topologies and see if I see the same effects, but I'm not
> > likely to have time for that for a couple days.
> > 
> > Thanks,
> > David
> > 
> > 
> > 
> 
> 
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