[gmx-users] Normalization in g_rdf

[Ondrej Marsalek]

Ah, now I see what you meant. Then it is fine. That is a separate
issue and is not really a problem for me.

Thank you,
Ondrej


On Tue, Nov 24, 2009 at 17:39, Berk Hess <gmx3 at hotmail.com> wrote:
> Hi,
>
> Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot
> is set from the initial frame.
> So if your volume fluctuates a lot, you might have incorrect normalization
> very close to the cut-off.
> But in "normal" liquid simulations the box length will never change more
> than 1%.
>
> Berk
>
>> Date: Tue, 24 Nov 2009 17:12:44 +0100
>> Subject: Re: [gmx-users] Normalization in g_rdf
>> From: ondrej.marsalek at gmail.com
>> To: gmx-users at gromacs.org
>>
>> Hi again,
>>
>> I thought pressure coupling is handled by g_rdf. Looking at the code,
>> it seems that the block starting with:
>>
>> /* Must init pbc every step because of pressure coupling */
>>
>> takes care of that, so even with a relatively big volume change at the
>> beginning, it should not be a problem. Is that not the case?
>>
>> Ondrej
>>
>>
>> On Tue, Nov 24, 2009 at 16:12, Berk Hess <gmx3 at hotmail.com> wrote:
>> > Hi,
>> >
>> > g_rdf limits the distance to half the minimum periodic image distance.
>> > So the volume normalization is always simply  4 pi r^2.
>> > It uses the starting unit-cell with a factor of 0.99.
>> > So you would only see strange effects when the box length reduces
>> > more than 1% due to pressure coupling.
>> >
>> > Berk
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