Re: How to generate the tcouple file for NAMD runs?

From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Oct 31 2010 - 08:23:46 CDT

Dear Catherine,

Use VMD. Load the coordinate (pdb or coor) file used in your namd config.
 From the extensions menu, open the TkCon window. Then (replacing text
between < > symbols with your desired values):

set allAtomsSel [atomselect top all]
$allAtomsSel set occupancy 0
set tcoupledAtomSel [atomselect top "<YOUR SELECTION TEXT FOR TEMP COUPLED
ATOMS>"]
$tcoupledAtomSel set occupancy <TEMP TO WHICH ATOMS SHOULD BE COUPLED>
$allAtomsSel writepdb tCoupledFile.pdb

Best,
Chris

2010/10/29 a a <patd_2_at_hotmail.com>

> Dear Sir/Madam,
>
> How to generate the tCouple file? e.g. if we need the following line in
> our configuration file.
>
>
> #tCoupleFile $fname.tCouple.pdb ### friction coef.=1.0
>
> What is the best way to generate the pdb file?
>
> Best regards,
>
> Catherine
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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