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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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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