[gmx-users] R: g_mindist on rhombic dodecahedron system

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 5 15:06:11 CEST 2011

Hi Anna,

The spikes going down to 0.1 nm can only be explained by a fragmented
representation of your protein in the frame. Mind that Gromacs does
not write molecules in one piece as it used to. You therefore have to
make all molecules whole prior to calling g_mindist. You mention doing
so, which raises the question what your actual command lines were, in
particular what you used as a reference structure. Or did you
accidentally use the original trajectory again, rather than the one
made whole? Please keep a record of the commands you used and paste
them in your mail so that we can better understand what may be
happening, rather than making (educated ;)) guesses.



On Tue, Jul 5, 2011 at 2:49 PM, Anna Marabotti
<anna.marabotti at isa.cnr.it> wrote:
> Dear users,
> can anybody give me suggestions about my questions below?
> Thank you very much
> Anna
> ________________________________
> Da: Anna Marabotti [mailto:anna.marabotti at isa.cnr.it]
> Inviato: lunedì 4 luglio 2011 17.43
> A: 'gmx-users at gromacs.org'
> Oggetto: g_mindist on rhombic dodecahedron system
> Dear users,
> following Tsjerk' suggestions, I simulate the protein which had some
> problems in periodic distance violations in a triclinic box, using instead a
> rhombic dodecahedron box created with the options:
> editconf -f prot.gro -o prot_boxdod.gro -bt dodecahedron -d 1.5 -c
> Minimization, PR-NVT and PR-NPT went OK (no error messages, potential energy
> after minimization of about -1e+6). I run 30 ns full MD (no PR).
> At the end of the production MD, I would like to repeat the g_mindist
> analysis, so I can be sure my system does not suffer again of a periodic
> distance violation.
> I performed g_mindist on 4 different systems, and these are my results:
> 1) on the resulting trajectory: on average, the distance between two
> periodic distances calculated on the entire protein (option = 1) is > 3 nm.
> However, until 10 ns I can see several "spikes" going down to < 0.1 nm
> 2) on the resulting trajectory, applying trjconv -pbc nojump before
> g_mindist: on average, the distance is < 0.1 nm
> 3) on the resulting trajectory, applying trjconv -pbc whole -ur compact
> before g_mindist: the same as 1) (perfectly superimposable)
> 4) on the resulting trajectory, applying trjconv -pbc whole -ur compact,
> then trjconv -pbc nojump, before g_mindist calculation: the same as 2)
> (perfectly superimposable)
> My questions are:
> 1) do I have to transform in some (other) way the trajectory before
> calculating g_mindist? Do I have to calculate g_mindist in another way (eg.
> using a different group for calculations)?
> 2) given these results, can I consider this trajectory suitable for
> analysis? (maybe excluding the first 10 ns)
> 3) If not, what can I do more to have a suitable trajectory?
> Many thanks for any suggestions, I'm quite frustrating for not understanding
> where the problem comes from...
> Anna
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
> "When a man with a gun meets a man with a pen, the man with the gun is a
> dead man"
> (Roberto Benigni, about Roberto Saviano)
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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