[gmx-users] PBC problem

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Wed May 16 06:55:58 CEST 2007

Thanks Tsjerk,
Probably because we use pressure coupling and the box size is deformed.

Best regards
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem

Hi Yuguang,

> 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}

This is not a rhombic dodecahedron.

> CRYST1   64.653   64.689   64.375  70.32 109.46  70.63 P 1           1

This shows that the second vector is larger than the first, thus
violating the gromacs rules for proper boxes (manual chapter 3;
although it could be handled a bit more liberally, especially in the
analysis tools).



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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