Re: New ABF order parameters

From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Tue Nov 20 2007 - 16:43:45 CST

Dear Jerome,

Two related questions:
The comment at the top of dihedral.tcl says:
# This code gets and returns degrees and kcal/mol/degree
# NAMD wants forces in kcal/mol/radian
Is this code fully integrated with NAMD - is this conflict of units resolved?

Since, the Jacobian correction = 0, is it correct to interpret the data in the outputFile as -kT*log P(theta), where P(theta) is the probability distribution along the dihedral order parameter?

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
>>

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