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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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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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