[gmx-users] pull DNA

[Maik Goette]

I think, you have to go more into detail...
I wouldn't expect DNA to unzip, if you just pull on the axis of the
helix for 1.2nm.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
        mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


qwp wrote:
> <%--AID_SENDTO_BEGIN--%>gmx-users<%--AID_SENDTO_END--%>
> hello everyone:
> i used the pull code in gromacs-3.2.1 to pull the dickerson DNA, use 
> ffamber94 force field. 
> i fixed six carbon atoms in one end(3 on each chain ), and pull six in 
> the other end of DNA.
> The velocity is 0.0004nm/ps. The k is 10000 kJ/(mol.nm.nm).i simulate 3ns.
> The DNA is stretched, but it isn't unzip.why ?
> thanks alot in advance. 
> <%--AID_EDIT_ATTACHMENT_BEGIN--%>
> <%--AID_EDIT_ATTACHMENT_END--%>
> <%--AID_FROMNAME_BEGIN--%>qwp<%--AID_FROMNAME_END--%>，<%-- 
> AID_FROMADDRESS_BEGIN--%>qi-wenpeng at mail.sdu.edu.cn<%--AID_FROMADDRESS_END--%> 
> <mailto:<%--AID_FROMADDRESS_BEGIN--%>qi-wenpeng at mail.sdu.edu.cn<%--AID_FROMADDRESS_END--%>>
> 2005-9-2
> 
> 
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