On 25/10/2011 5:29 PM, James Starlight wrote:
This was due to that in .gro file corresponded to the end of
productive MD I've found this
http://i1209.photobucket.com/albums/cc394/own11/mdL.png
It's looks like the protein moved out from box so I've thought that
some error occured during stimul
This was due to that in .gro file corresponded to the end of productive MD
I've found this http://i1209.photobucket.com/albums/cc394/own11/mdL.png
It's looks like the protein moved out from box so I've thought that some
error occured during stimulation
>>
> I don't understand this statement. You
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 d
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 ?
2- Why the pereodic
James Starlight wrote:
Justin, hello!
I have forced with some problem during final stage of your turorial.
I dont know why but after NPT phase my sytem has occured in the standart
cubic box instead of dodecahedron (after all previosly phases my system
was in correct box).
So when I've pa
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