[gmx-users] trjconv -pbc?

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 21 22:37:19 CEST 2007


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



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