[gmx-users] extended bonds

[Mark Abraham]

Are they whole in the .tpr?

Mark


On Wed, Apr 2, 2014 at 8:31 PM, pratibha <kapoorpratibha7 at gmail.com> wrote:

> Hi all
>
> I have done simulations of my protein in water-cosolvent system (random
> initial addition) at 450K. At the end I have used:
> trjconv -f *.xtc -s *.tpr -center -pbc whole -o new.xtc
> But when I view my trajectory in vmd, I can see extended intramolecular
> bonds between cosolvent molecules. This problem usually come when pbc is
> not
> taken care off. But in my case I have used trjconv (as above) to account
> this. Is there something wrong in my simulations? I have never encountered
> such problem before at lower temperature of 300K.
> If needed I can attach my *.mdp file.
>
> Thanks in advance.
>
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