[gmx-users] trjconv -pbc?

[bmmothan at ucalgary.ca]

Hi TSjerk,

Thanks for the explaination. It is appreciated.

Belquis



> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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