[gmx-users] RE: Justin umbrella sampling tutorial...... (rama david)

[Du Jiangfeng (BIOCH)]

For your second problem: you have to create this file by writing the group numbers, which inform the script to decide which two groups to be selected for distance calculation. 

If you made it, you first problem would probably be solved.

Good luck,
Jiangfeng.

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands


Message: 4
Date: Wed, 23 May 2012 19:18:56 +0530
From: rama david <ramadavidgroup at gmail.com>
Subject: [gmx-users] Justin umbrella sampling tutorial......
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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        <CAD=-SYHie5KxqJ9fgdHQyKqAV0VUSYc-atshBLgS5CQiRFuNaQ at mail.gmail.com>
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Hi Gromacs Friends,

   I am performing justin tutorial for umbrella sampling ..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
I encounter with following problem while using the disatances.pl script

1. After command perl distances.pl  I got following message ...


   Use of uninitialized value $distance in concatenation (.) or string at
distances.pl line 30.
   readline() on closed filehandle IN at distances.pl line 16.
  What may be reason for these ..
2. What is the groups.txt ??
   Where it will find ?? Why it is needed??
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