From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Tue Apr 06 2010 - 12:12:44 CDT
Hi Marcello,
I have double-checked your modification on yesterday's version and it
works: it gives the same results as namd2.6 version for few MD steps
with amber ff.
I would guess and say that you can also initialize numenerentries=0 in
Parameters::initialize() member function. I don't know if numenerentries
values
have any influence on standard ff simulations since they appear to be
used in tabulated modified LJ potentials.
All the best,
George
Marcello Sega wrote:
> Dear all,
>
> I also had the same problem trying to use amber files with 2.7b2. I
> had a cursory look at the code and it seems that the problem is the
> variable numenerentries (Parameteres.C), which is never initialized
> when reading amber parameters.
>
> To me the quick fix
>
> Parameters::Parameters(Ambertoppar *amber_data, BigReal vdw14)
> {
> initialize();
> numenerentries=0;
> // Read in parm parameters
> read_parm(amber_data,vdw14);
> }
>
> in the constructor for reading amber parameter data did the job (i.e.
> a simple test run gives the same results using b2 and b1)
>
> *Beware* that I'm not sure if this is a proper solution or if on the
> contrary it breaks something else (I'm using namd only since a couple
> of days, and I don't know the internals: mine is just a wild guess) so
> use it at your own risk...
>
> Maybe somebody else could check this?
>
> Cheers,
>
> Marcello
>
>
>
>
>
> On Wed, Mar 31, 2010 at 2:02 PM, Vlad Cojocaru <Vlad.Cojocaru_at_h-its.org> wrote:
>
>> Dear Peter,
>>
>> I did not have the time to further test new CVS codes but if you still have
>> the problem with the newest CVS codes .. I am afraid that the problem is not
>> fixed yet.
>> I post my reply to the list as well maybe there are some updates from the
>> NAMD developers on this .. Of course, this problem is a very important one
>> for everybody who is using NAMD with AMBER ff ..
>>
>> Cheers
>> Vlad
>>
>> Peter Schmidtke wrote:
>>
>>> Dear Vlad,
>>>
>>> I saw your posts on the namd mailing list and wondered if you finally
>>> solved the problem, I have the same right now and I did not find any
>>> follow
>>> up of the problem on the namd mailing list.
>>> The amber ff part of my conf file looks like this :
>>>
>>> amber on
>>> parmfile ../s_comp1.top
>>> ambercoor ../s_comp1.crd
>>> outputname s_comp1_min
>>> exclude scaled1-4
>>> 1-4scaling 0.833333
>>>
>>> where s_comp1.top is a amber topology, and the crd file is an amber
>>> coordinate file. Like in your case it yields a segmentation fault during
>>> the starting phase.
>>>
>>> Thanks in advance for your help
>>>
>>> Best regards.
>>>
>>>
>>>
>>>
>> --
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> Heidelberg Institute for Theoretical Studies
>> HITS gGmbH
>> Molecular and Cellular Modelling Group
>> Schloss-Wolfsbrunnenweg 35
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533202
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]h-its.org
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> Amtgericht Mannheim / HRB 337446
>> Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter
>> http://www.h-its.org (http://eml-research.de)
>> ----------------------------------------------------------------------------
>>
>>
>>
>
>
>
>
-- ________________________________________________________________________ George Madalin Giambasu PhD Student University of Minnesota Phone : (612) 625-6317 Department of Chemistry Fax : (612) 626-7541 207 Pleasant St. SE e-mail: Minneapolis, MN USA 55455-0431 GeorgeMGiambasu_at_umn.edu York Research Group giambasu_at_gmail.com http://theory.chem.umn.edu/~giambasu ________________________________________________________________________
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