[gmx-users] PBC problem

[Mu Yuguang (Dr)]

Hi all,
We found some problems in using g_dist or g_minidist to calculate distance in some  PBC condition, dodecahedron
The output is as followed:

Back Off! I just backed up mindist.xvg to ./#mindist.xvg.2#
Warning: Triclinic box is too skewed.
         Box (3x3):
            Box[    0]={ 6.46530e+00,  0.00000e+00,  0.00000e+00}
            Box[    1]={ 2.14552e+00,  6.10274e+00,  0.00000e+00}
            Box[    2]={-2.14464e+00,  3.05200e+00,  5.24664e+00}
         Can not fix pbc.

The input pdb is like this
REMARK    GENERATED BY TRJCONV
TITLE     Protein in water t= 394.00003
REMARK    THIS IS A SIMULATION BOX
CRYST1   64.653   64.689   64.375  70.32 109.46  70.63 P 1           1
MODEL        0
ATOM    201  C1'  RA     7      13.130  -2.870  23.080  1.00  0.00
ATOM    553  O4'  RU    18      44.730  54.920  28.830  1.00  0.00


Best regards
Yuguang
 
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Milan Melichercik
Sent: Wednesday, August 23, 2006 7:50 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein in bilayer

Dňa St 23. August 2006 13:42 mahbubeh zarrabi napísal:
> dear itamar
> where is adress make-hole site?
> thanks

3rd record on following page
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,5/
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