[gmx-users] extended bonds

[pratibha]

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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