Re: NANMA free energy surface vacuum map problems

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Nov 02 2010 - 05:40:08 CDT

Hi guys,

Could that possibly be a problem of CMAP vs. no CMAP?

Jerome

On 2 November 2010 02:33, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> 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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