Re: ABF : dihedral-com.tcl

From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Wed Nov 21 2007 - 11:16:37 CST

Vlad,

That worked, thanks! Chris, is it still necessary to edit abf_script.tcl? This change is to be made on line #330 of abf_script.tcl, correct?

Vaithee

---- Original message ----
>Date: Wed, 21 Nov 2007 17:36:37 +0100
>From: Chris Chipot <Christophe.Chipot_at_edam.uhp-nancy.fr>
>Subject: Re: ABF : dihedral-com.tcl
>To: Subramanian Vaitheeswaran <vaithee_at_umd.edu>
>Cc: namdlist <namd-l_at_ks.uiuc.edu>
>
>Dear Vaithee,
>
>this new order parameter requires updating the ABF driver, i.e.
>abf_script.tcl:
>
>...
> if {(($coordinate == "dihedral") ||
> ($coordinate == "dihedral-com")) &&
> ($forceConst > 0.0) &&
> (($xi < $xiMin) ||
> ($xi >= $xiMax))}
>...
>
>
>Chris
>
---- Original message ----
>Date: Wed, 21 Nov 2007 17:36:31 +0100
>From: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
>Subject: Re: namd-l: ABF : dihedral-com.tcl
>To: Subramanian Vaitheeswaran <vaithee_at_umd.edu>
>Cc: NAMD list <namd-l_at_ks.uiuc.edu>
>
>Dear Vaithee,
>
>You need to edit the abf.tcl startup script in order to add the abf0 and
>abf3 keywords.
>
>Either you add "abf0 {}" and "abf3 {}" in "array set defaults"
>(the same way abf2 is defined there)
>
>Or you add them in "set silent ....." (just add "abf0" and "abf3" after
>"direction")
>
>Cheers
>vlad
>
>Subramanian Vaitheeswaran wrote:
>
>>Dear Jerome and other ABF developers,
>>
>>Another question, about dihedral-com.tcl this time. Following the ABF website, I identified the four groups of atoms defining the dihedral as:
>>abf abf1 {6 7}
>>abf abf2 {8 9}
>>abf abf3 {14 15}
>>abf abf4 {16 17 18 19 20}
>>in my input conf file. This dies with the error:
>>TCL: Unknown ABF keyword: abf3
>>FATAL ERROR: Unknown ABF keyword: abf3
>>
>>It seems from dihedral-com.tcl that the group numbering should run from abf0-abf3 instead of 1-4, but this doesn't help either. Then it complains about:
>>TCL: Unknown ABF keyword: abf0
>>FATAL ERROR: Unknown ABF keyword: abf0
>>
>>What is the correct usage?
>>
>>thanks,
>>Vaithee
>>
>>---- Original message ----
>>
>>
>>>Date: Tue, 20 Nov 2007 17:07:01 -0500
>>>From: "Jerome Henin" <jhenin_at_cmm.chem.upenn.edu>
>>>Subject: Re: New ABF order parameters
>>>To: "Subramanian Vaitheeswaran" <vaithee_at_umd.edu>
>>>Cc: namdlist <namd-l_at_ks.uiuc.edu>, abf_at_edam.uhp-nancy.fr
>>>
>>>Dear Vaithee,
>>>
>>>Thanks for your message, this is a mistake in the documentation. The
>>>list of 4 atom indices should be passed through the parameter abf1:
>>>abf abf1 "4 5 1 2"
>>>
>>>Best,
>>>Jerome
>>>
>>>
>>>On Nov 20, 2007 4:56 PM, Subramanian Vaitheeswaran <vaithee_at_umd.edu> wrote:
>>>
>>>
>>>>Dear ABF and NAMD developers,
>>>>
>>>>I downloaded the files dihedral.tcl and dihedral-com.tcl into ~/NAMD_2.6_Linux-i686/lib/abf from the ABF website. Do I need to do any thing else to use these new order parameters?
>>>>
>>>>When I run a test job with "abf coordinate dihedral", it dies with the error:
>>>>TCL: Unknown ABF keyword: abf3
>>>>FATAL ERROR: Unknown ABF keyword: abf3.
>>>>
>>>>Here is the ABF part of my conf file:
>>>>#######################################################
>>>>## ABF ##
>>>>#######################################################
>>>>if {1} {
>>>>source ~/NAMD_2.6_Linux-i686/lib/abf/abf.tcl
>>>>abf coordinate dihedral
>>>>abf abf1 {6}
>>>>abf abf2 {8}
>>>>abf abf3 {14}
>>>>abf abf4 {16}
>>>>abf dxi 0.1
>>>>abf xiMin 0.1
>>>>abf xiMax 179.9
>>>>abf outFile abf_AA.pmf
>>>>abf historyFile abf_AA.hist
>>>>abf fullSamples 200
>>>>abf inFiles {}
>>>>abf dSmooth 0.0
>>>>abf restraintList {}
>>>>#######################################################
>>>>Any help in fixing this problem is much appreciated.
>>>>
>>>>thanks,
>>>>Vaithee
>>>>
>>>>
>>>>
>>
>>
>>
>>
>
>--
>----------------------------------------------------------------------------
>Dr. Vlad Cojocaru
>
>EML Research gGmbH
>Schloss-Wolfsbrunnenweg 33
>69118 Heidelberg
>
>Tel: ++49-6221-533266
>Fax: ++49-6221-533298
>
>e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
>http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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