[gmx-users] trjconv -pbc?

[Tsjerk Wassenaar]

Hi Belquis,

Just some background on the issue. The reason that your solution
worked, and therefore the failure of your first procedure, is that in
the second case the frame at t=10ns was modified using the frame at
t=10-timestep ns as reference, whereas the modification in the first
case was done using t=0ns as the reference. In 10 ns a lot of
translation and rotation happens, making the routine for removing
jumps over periodic boundaries inadequate.

Cheers,

Tsjerk

On 6/21/07, bmmothan at ucalgary.ca <bmmothan at ucalgary.ca> wrote:
> Hi Tsjerk,
>
> Thank you for replying. I did give it a reference structure where the two
> parts are together. I solved the problem finally!
> I had a 10ns simulation before that and I used -pbc nojump on the original
> trjactory and it worked fine..but when I did it for the extra 10 ns i ran,
> it didnt work out. It only worked out when I joined the two 10ns original
> trjactories and used -pbc nojump.
>
> Thank you
>
> Belquis
>
>
>
> > Hi Belquis,
> >
> > You have to give trjconv a reference structure in which the parts are
> > together and which is close to the starting configuration. This has
> > been mentioned on the list before. For more information, search the
> > archives on trjconv and/or periodic boundary conditions (and possibly
> > my name).
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 6/21/07, bmmothan at ucalgary.ca <bmmothan at ucalgary.ca> wrote:
> >> Hello all,
> >>
> >> I have tried using trjconv -pbc(all options) to get a continuous
> >> trjactoary visulations on VMD.  I am modeling an 11 residue receptor
> >> antiparellel to itself and one of the receptor strand jumps outside the
> >> box sometimes.
> >>
> >> I have used search to solve the problem but everthing i tried didnt
> >> work
> >> and the -pbc just makes it worse.
> >>
> >> I tried using the -pbc nojump alone and this made my two receptor
> >> strands
> >> away from each other all the way (one inside and one outside the box).
> >> However i want them to be close together since they are hydrogen
> >> bonded.
> >>
> >> I have also tried: nojump then whole; whole then nojump and they make
> >> the
> >> receptor just fly around or pieces of it stretch.
> >>
> >> anyhelp is appreciated.
> >>
> >> Belquis
> >>
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> > _______________________________________________
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> >
> >
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623