Re: NANMA free energy surface vacuum map problems

From: Carles Corbi Verge (ccorbi_at_ugr.es)
Date: Mon Nov 01 2010 - 06:16:36 CDT

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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