[gmx-users] PBC problem

[Mu Yuguang (Dr)]

Hi Tsjerk,
Thanks. I will try that.

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 Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 4:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem

Hi Yuguang,

Gromacs should automatically fix the box to meet the requirements
during an mdrun with pressure coupling (but does sometimes fail).
There is also a certain tolerance in gromacs for the deviations.

Anyway.., you can download a version of GMX3.2.1 from
http://nmr.chem.uu.nl/~tsjerk/GMX/gromacs-3.2.1-rtc.tgz
in which I modified editconf.c (and pbc.c/pbc.h) to have an option for
changing any triclinic box into a box which conforms to the gromacs
rules. Maybe you just want to get the parts of the code involved and
transfer them to GMX3.3.1, which should be quite straightforward. The
developers are welcome to incorporate the option/code if they like to
include it. The editconf option I added is -fix. Note that editconf
will still issue a warning about the skewness of the box, but on a
'fixed' structure, that should not occur anymore.

Hope it helps,

Tsjerk


On 5/16/07, Mu Yuguang (Dr) <YGMu at ntu.edu.sg> wrote:
> Thanks Tsjerk,
> Probably because we use pressure coupling and the box size is
deformed.
>
> 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 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).
>
> Cheers,
>
> Tsjerk
>
>
> --
> 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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-- 
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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