[gmx-users] deformation in cnt

Atila Petrosian atila.petrosian at gmail.com
Wed Dec 4 16:48:28 CET 2013

Dear Justin

Thanks for your reply

z dimension of box is exactly equal to the length of
the cnt axis.

> The box size should be (length of CNT) + (bond length).

What value is appropriate for bond length to add length of CNT?

So, using freeze is not suitable for my system (neither in the em step nor
in the nvt equilibration step)? Is my opinion true?

I have a general question:
When can I use freeze? What is difference between freeze and position
restraint? Which of them is good for my system (cnt containing systems).

Best wishes

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