James Starlight wrote:
Justin,
I've used trjconv -pbc mol -ur compact
but the final picture was still wrong :(
So I think that something happened with my box because
1- If the cubic representation is set on default why other .gro
structures were visualized in VMD in dodecahedral box on default ?
VMD always defaults to a triclinic representation (since that is what is stored
in Gromacs by default) unless the PBC is wrapped with -pbc mol -ur compact. If
VMD truly produces the pseudospherical shape, then trjconv was invoked somewhere
along the way.
2- Why the pereodic boundaries were distorded in the next stage after
NPT (production MD) that my structure were outside the box on half ? I
want to point that on MD stage the box were dodecahedral again like in
the NVT and other stages but my structure was in wrong position.
I don't understand this statement. You should also note that a periodic box has
no "outside." Perhaps it would be useful to post images online. If you choose
to do so, please follow bullet point #4 here:
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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