[gmx-users] pull DNA

qwp qi-wenpeng at mail.sdu.edu.cn
Tue Sep 6 13:09:13 CEST 2005

Hi Maik Goette,

Thank you very much for the reply. I will simulate for a longer time, for few days I will stend the results to you !

thanks a lot for the help!

Qi Wenpeng,qi-wenpeng at mail.sdu.edu.cn
----- 收到以下来信内容 ----- 
发件人: Maik Goette 
收件人: qi-wenpeng,Discussion list for GROMACS users 
时  间: 2005-09-06, 18:45:27
主  题: Re: [gmx-users] pull DNA

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.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.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_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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