[gmx-users] Questions in using non-equilibrium dynamics

qwp qi-wenpeng at mail.sdu.edu.cn
Fri Sep 2 14:29:53 CEST 2005

Hello everyone:

I set a system which has only 2 C atoms, and there is only a special modified interaction.(which kb=100 b0=0.142 and there is no LJ interaction)
In my *.mdp file I set these paraeters
acc-grps                 = a_1
accelerate               = 0.0 0.0 1.0
freezegrps               = a_2
freezedim                = Y Y Y
cos-acceleration         = 0
in a_1 groug there is a C atom.I think the external force added is F(add)= m*a=12*1.0 (kJ/mol/nm),is it right?

I simulate this simple system for 10 ns and from the 3th ns the coordinates of the 2 carbon atoms is not changed. Beacouse of there is a pretty small kb, the  the bond is elongated. Then I calculated the force of the bond.It must be F(bon)= kb(newlength - b0).Is it right?

There is a very interested reslut , the F(add)=12 pN the F(bon)=6.7 pN. But the a_1 atom doesn't move for nearly 7 ns, it must be in equilibrium state.

why? Can anyone tell me the reason.

Thank you !

Qi Wenpeng,qi-wenpeng at mail.sdu.edu.cn
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050902/a76f230a/attachment.html>

More information about the gromacs.org_gmx-users mailing list