[gmx-developers] Re: [gmx-users] 'the reciprocal space calculation will not necessarily cancel'

[Justin Lemkul]

On 5/16/13 7:54 AM, Floris Buelens wrote:
> Hi,
>
> I received no reply on the users list, could anybody enlighten me on the warning message in the email below?
> thanks!
>

The warning was made more clear before version 4.6.1; I assume you are using 
4.6?  There is discussion of what is going on at 
http://redmine.gromacs.org/issues/1146.  The change Berk implemented created a 
totally new warning message with more explicit information:

http://redmine.gromacs.org/projects/gromacs/repository/revisions/a46b7f1f2f380c7238fe63bce706078343c9210e/diff/src/kernel/readir.c

-Justin

>
> ----- Original Message -----
> From: Floris Buelens <floris_buelens at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Cc:
> Sent: Tuesday, 14 May 2013, 14:02
> Subject: [gmx-users] 'the reciprocal space calculation will not necessarily
> 	cancel'
>
> Hi,
>
> I'm not clear on the meaning and implications of this warning message from grompp:
>
> WARNING 1 [file ../md.mdp]:
>
>    With coulomb soft core, the reciprocal space calculation will not
>    necessarily cancel.  It may be necessary to decrease the reciprocal space
>    energy, and increase the cutoff radius to get sufficiently close matches
>    to energies with free energy turned off.
>
> Can anybody help me understand this better? In what context are we talking about cancellation? Around a thermodynamic cycle, or in a more narrow sense? Why would we not see such a cancellation?
>
> In my understanding, if we have an A state with a certain set of charges and a B state with another, the end states at lambda=0 and lambda=1 should match exactly what you would see if you evaluated the A and B states independently without using the free energy code. Soft core vdW or coulomb would only affect the shape of the pathway connecting them and not the end points. So I'm having trouble seeing what kind of cancellation we're relying upon.
>
> Thanks in advance for any insights!
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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