From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Nov 02 2010 - 07:23:30 CDT
That's a very interesting point. I hadn't even noticed the files being
distributed with the ABF tutorial (and FEP for that matter) don't include
CMAP. Looking at Tobias and Brooks (1992), their PMF is similar to the one
in the tutorial though and they obviously didn't have CMAP. Interestingly,
the one in your colvars paper is a bit closer to what I found (although the
C7ax is still slightly lower in energy). I'll look into this further when a
I get a chance.
JC
-----Original Message-----
From: heninj_at_gmail.com [mailto:heninj_at_gmail.com] On Behalf Of Jérôme Hénin
Sent: Tuesday, November 02, 2010 5:40 AM
To: JC Gumbart
Cc: Carles Corbi Verge; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: NANMA free energy surface vacuum map problems
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
>
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:19 CST