From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Nov 01 2010 - 20:33:14 CDT
Indeed, as you'll see in the provided png files, I saw the same thing. I'm attributing it to a sampling issue (taking the easy way out!), but I wanted to be sure the simulations as given could be completed in a relatively short time. Probably it would be a good for you to run them longer to see if the PMF improves relative to Fig. 5A.
JC
On Nov 1, 2010, at 6:16 AM, Carles Corbi Verge wrote:
> Hi Jérôme,
>
> I'm not talking about of a new simulation, I'm using the input files of the tutorial, actually I use the example-output files to build the map. I merged the outputs I then I run abf_integration following the instructions of the tutorial. In this map the C7ax spot have around 3 kcal/mol more than the alphaL area.
>
> Best,
> Carles.
>
>
>
> El 29/10/2010, a las 16:33, Jérôme Hénin escribió:
>
>> Hi Carles,
>>
>> This could be a convergence issue. Is the (phi,psi) map well-sampled?
>> Did you visualize the histogram (.count file)?
>>
>> Best,
>> Jerome
>>
>> On 29 October 2010 15:03, Carles Corbi Verge <ccorbi_at_ugr.es> wrote:
>>> Dear NAMD users,
>>> I downloaded the files of the ABF tutorial, I started to follow the case 3,
>>> isomerization of N-acetyl-N'-methylalanylamide ( NANMA ). With the results
>>> files you find in the namd website I try to reproduce the energy surface map
>>> of ABF simulations in vacuum. I merged them, then I run the abf_integration
>>> script, and The map I get is pretty different to the figure 5.a in the
>>> tutorial . The second minima appears in the region [48,52] instead the C7ax
>>> region [70,-80] . Is it that possible? Any suggestions?
>>> Best Regards,
>>>
>>> Carles Corbi Verge
>>>
>>> Departamento de Química Física.
>>> Facultad de Ciencias.
>>> Universidad de Granada.
>>> 18071 Granada, SPAIN
>>> Tel: (+34) 958 240437
>>> Fax: (+34) 958 272879
>>>
>>>
>>>
>>>
>>>
>>
>
> Carles Corbi Verge
>
>
> Departamento de Química Física.
> Facultad de Ciencias.
> Universidad de Granada.
> 18071 Granada, SPAIN
>
> Tel: (+34) 958 240437
> Fax: (+34) 958 272879
>
>
>
>
>
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