[gmx-users] how to stretch a molecule

qiwenpeng at sinap.ac.cn qiwenpeng at sinap.ac.cn
Tue Dec 13 12:35:11 CET 2005

hello all!

I want to stretch a DNA molecule, but which method shoud I use ?

the  afm? constraint? or constant acceleration?

but every method has some problems.

i.e. add the acceleration on some atoms. I have to (1)freeze some atoms at the other end (2)and set the parameter comm-mode= linear. When stretching, they conflict with each other. the result is completely wrong. Use afm is in the same situation.

constraint may be better.but the result can not compared with other paper.

Thank you very much for kindly replys
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