VMD-L Mailing List

From: Valeria Molinero (valeria.molinero_at_utah.edu)
Date: Mon Aug 11 2008 - 11:40:45 CDT

John,

the new version you compiled seems to produce the right g(r). Thanks!

May I ask how it is computing the volume that is using to normalize
the g(r)?
I remember there was something fishy with it before and i wonder if this
version fixed it.

thanks you very much for your help,
vale

On Aug 6, 2008, at 10:24 AM, John Stone wrote:

> Valeria,
> I've posted the new test build on the VMD Public project on
> BioCoRE. Please try it out and let us know if this solves
> the problem you had been having. If you haven't downloaded test
> builds before, please see this page:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Aug 03, 2008 at 06:00:27PM -0600, Valeria Molinero wrote:
>> John,
>> thanks so much. I am looking forward to it.
>> cheers,
>> vale
>>
>> On Jul 31, 2008, at 12:00 PM, John Stone wrote:
>>
>>>
>>> I should have a new test build containing Axel's patch available
>>> pretty shortly. I'll let you know when it's posted.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Tue, Jul 22, 2008 at 05:58:25PM -0600, Valeria Molinero wrote:
>>>> Axel,
>>>>
>>>> where i can get the version you mention? I am using version 1.8.6
>>>> for
>>>> mac intel.
>>>>
>>>> The bin size I use is 0.1A. In the version I have I must use a
>>>> small
>>>> bin because
>>>> the volume used in the normalization is not the one of a sphere
>>>> shell
>>>> but its
>>>> limiting value 4 pi r^2 binsize. Is this what you fixed?
>>>>
>>>> thanks for your help,
>>>> vale
>>>>
>>>> On Jul 22, 2008, at 4:06 PM, Axel Kohlmeyer wrote:
>>>>
>>>>> if you download a recent alpha test version for the next VMD
>>>>> release, gofr calculations should work fine.
>>>>
>>>> ______________________________
>>>>