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

[Anna Marabotti]

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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