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: [email protected] 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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