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

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Jul 5 14:49:16 CEST 2011

Dear users,
can anybody give me suggestions about my questions below? 
Thank you very much


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 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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