Re: NANMA free energy surface vacuum map problems

From: Carles Corbi Verge (ccorbi_at_ugr.es)
Date: Thu Nov 04 2010 - 09:37:34 CDT

Hi guys,

I run NANMA ABF simulations with and without CMAP correction, with the CMAP I get the second minima in C7ax conformation, but in the no CMAP simulations, doesn't matter if the simulations are much longer, the second minima is in the alphaL region.

Thanks a lot for your help!.

Best,
Carles.

El 02/11/2010, a las 14:18, Jérôme Hénin escribió:

> Just to explain where I am coming from: traditionally, I would not use
> CMAP for NANMA because that correction explicitly targets protein
> conformation, and is knowledge-based (PDB) rather than physics-based.
> So I thought its relevance in the case of NANMA was not established.
>
> But on second thought, looking back at the CMAP papers, it does seem
> to make NANMA agree better with QM/MM sampling, so it does seem to be
> a good idea to include it. My bad.
>
> Jerome
>
> On 2 November 2010 13:23, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>

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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