Re: ABF tutorial

From: sudipta (sudipta.mml_at_gmail.com)
Date: Tue Jul 21 2009 - 05:39:03 CDT

Dear Chris Chipot,

           Thanks for our reply. ok, I shall generate these files by running
energy-minimization and equilibration .
Thanks & regards
Sudipta

On Mon, Jul 20, 2009 at 7:39 PM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:

> Sudipta,
>
> the ABF tutorial assumes, perhaps erroneously so, that the user is
> capable, given a PSF and a PDB file, of running an equilibration.
> Not being sure of this assumption, we have, nonetheless, provided in
> a separate directory, two "vanilla" NAMD configuration files written
> for the purpose of energy-minimization and equilibration.
>
> Regards,
>
> Chris Chipot
>
>
> sudipta a écrit :
>
>> Hi All,
>>
>>
>> I want to run ABF simulation of decaalanine that has given in tutorial
>> file. But I have not got all the required file in tutorial directory. The
>> files which I have not got are
>>
>> COORDINATES
>>
>> coordinates reference_0.coor
>> bincoordinates reference.coor
>>
>>
>> # VELOCITIES
>>
>> velocities reference_0.vel
>> binvelocities reference.vel
>>
>> Can anyone please suggest me where from I get or generate these file.
>>
>> Thanks & regards
>> Sudipta
>>
>
>
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> on leave from Nancy Université, CNRS
> Theoretical and Computational Biophysics Group
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 North Mathews Phone: (217) 244-5711
> Urbana, Illinois 61801 Fax: (217) 244-6078
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_edam.uhp-nancy.fr
> Web: http://www.ks.uiuc.edu
> http://www.edam.uhp-nancy.fr
>
> I disapprove of what you say, but I will defend to the death your right
> to say it
> Evelyn Beatrice Hall
> _______________________________________________________________________
>

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