[gmx-users] soft-core and coulomb transformation

[bharat v. adkar]

Hi,
   I can see the curves getting overlapped after the code-modification 
suggested by Berk for ethane to methane coulomb transformations in forward 
and reverse directions.

Thanks Berk and David.

bharat


On Wed, 14 Nov 2007, bharat v. adkar wrote:

>
> 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" <dmobley at gmail.com>
>> >  Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >  To: "Discussion list for GROMACS users" <gmx-users at 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" <dmobley at gmail.com>
>> > > >  Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > > >  To: "bharat v. adkar" <bharat at sscu.iisc.ernet.in>
>> > > >  CC: Discussion list for GROMACS users <gmx-users at 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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>
>

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