[gmx-users] Lyzosyme with ligand tutorial

[James Starlight]

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 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.


James

2011/10/24 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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 passed my system in the MD stage- it's moved back into normal
>> dodecahedron box but on the placement where previously system was. So as the
>> consequence I've obtained protein in the wrong place ( some of its parts
>> were outside new box )
>>
>> I've tried examined why this might occur but have not found possible
>> explanations.
>>
>> I've examined box coordinates of the all .gro structurs obtained after
>> each of the stages and all of them contained such box vectors
>> 7.85059   7.85059   5.55120   0.00000   0.00000   0.00000   0.00000
>> 3.92529   3.92529
>>
>> As I understood It's correspond to the system in the dodecahedron box but
>> my ntp.gro structure with the same is in the cubic box ( with the above box
>> coordinates as well). Why its might occured and were else information of the
>> box coordinates is present exept of initial structure gro file ?
>>
>>
> You still have a dodecahedral box.  The default representation is a simple
> triclinic cell.  A true compact representation can be obtained with:
>
> trjconv -pbc mol -ur compact
>
> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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