From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Aug 13 2009 - 10:16:12 CDT
Hi Jim, Hi Chris, namd users,
Just to let you know, my tcl scripts work now fine with the namd
compiled today from cvs . No unpredictable initialization of the
alchemical module occurs ...
Thanks and best wishes
Vlad
Jim Phillips wrote:
>
> The variable to turn on TI was uninitialized when alchemy was not on,
> so it was probably starting out non-zero in some unpredictable set of
> cases. I haven't actually reproduced the problem, but it should be
> fixed now. Please test tomorrow after the nightly build and cvs update.
>
> Thanks for reporting this.
>
> -Jim
>
>
> On Mon, 10 Aug 2009, Brian J. Bennion wrote:
>
>> Hello All
>> This same error or a similar one occurs if you request a number of
>> cpus at least as great as 2048.
>> TI automagically pops on and dies because there are no other
>> parameters to support is operation.
>> I was just using the apoa1 benchmarck compound to test my namd2.7b
>> from cvs July 24th 11:50am.
>>
>>
>> Brian
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>> Behalf Of Cojocaru,Vlad
>> Sent: Saturday, August 08, 2009 3:53 PM
>> To: George Madalin Giambasu; namd-l_at_ks.uiuc.edu
>> Subject: RE: namd-l: namd27: tclforces activate TI calculation by
>> default
>>
>> Hi George,
>>
>> I see exactly the same problem .... Don't have a solution yet .. I
>> reported this already ..
>>
>> If you find a way to deal with it, let me know
>>
>> Ceau
>>
>> Vlad
>>
>> P.S. Toate cele bune :))
>>
>>
>> -----Original Message-----
>> From: owner-namd-l_at_ks.uiuc.edu on behalf of George Madalin Giambasu
>> Sent: Sat 8/8/2009 11:12 PM
>> To: namd-l_at_ks.uiuc.edu
>> Subject: namd-l: namd27: tclforces activate TI calculation by default
>>
>> Hi,
>>
>> This applies to the latest cvs namd27 version (Aug 7th): when trying to
>> use tclforces (eg constraining a bond lentgh) namd activates the TI
>> calculation and dies immediately, without any outputed eror . This
>> happens for a regular plain NPT MD simulation.
>>
>> Forcing "alch off" in the input doesn't change anything.
>>
>> g++
>>
>> --
>> ________________________________________________________________________
>> 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/
>> ________________________________________________________________________
>>
>>
>>
>>
>>
>
-- ---------------------------------------------------------------------------- Dr. Vlad Cojocaru EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Tel: ++49-6221-533202 Fax: ++49-6221-533298 e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------
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