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

[David van der Spoel]

On Fri, 2005-09-02 at 20:29 +0800, qwp wrote:
> <%--AID_SENDTO_BEGIN--%>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.
Are you sure you aren't using constraints?
>  
>  
> Thank you !
> <%--AID_EDIT_ATTACHMENT_BEGIN--%>
> <%--AID_EDIT_ATTACHMENT_END--%>
> <%--AID_FROMNAME_BEGIN--%>Qi Wenpeng，<%--AID_FROMADDRESS_BEGIN--%>qi-
> wenpeng at mail.sdu.edu.cn<%--AID_FROMADDRESS_END--%>
> 2005-9-2 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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